EPA Estuarine Coastal Waters Tech Guidance 2000

United States Office of Water EPA-822-B-00-024
Environmental Protection 4304 December 2000

Agency Washington, D.C. 20460
Estuarine and Coastal Marine

Waters: Bioassessment and
Biocriteria Technical Guidance
Estuarine and Coastal Marine Waters:
Bioassessment and Biocriteria Technical Guidance
George R. Gibson, Jr., Project Leader (4304)

USEPA
Office of Water
Office of Science & Technology
1200 Pennsylvania Avenue, NW
Washington, DC 20460
Principal Authors:
Michael L. Bowman Jeroen Gerritsen

Principal Scientist Principal Scientist
Tetra Tech, Inc. Tetra Tech, Inc.
10045 Red Run Boulevard, Suite 110 10045 Red Run Boulevard, Suite 110
Owings Mills, MD 21117 Owings Mills, MD 21117
George R. Gibson, Jr. (4304) Blaine D. Snyder

USEPA Senior Scientist
Office of Water Tetra Tech, Inc.
Office of Science & Technology 10045 Red Run Boulevard, Suite 110
1200 Pennsylvania Avenue, NW Owings Mills, MD 21117
December 2000
This document is dedicated to the memory of Dr. Douglas Farrell of the
Florida Department of Environmental Protection and Dr. Donald Lear, U.S.
Environmental Protection Agency (retired). It is fitting that this effort to which they
volunteered so much of their invaluable experience and expertise be so dedicated.
The benthic community index which Doug developed is also cited here as the
“Farrell Index” in further recognition of his unselfish contribution to the protection
and management of our coastal resources. Much of the methodology described in
the coastal survey portion of this guide was developed from Don Lear’s pioneering
efforts.
The contributors to this manual sincerely hope that the good common sense,
attention to scientific veracity, and practical application of the information to
protect our marine resources - so ably personified by Don and Doug - is adequately
reflected in these pages.
Disclaimer
This manual provides technical guidance to States, Indian tribes and other authorized
jurisdictions to establish water quality criteria and standards under the Clean Water Act
(CWA), to protect aquatic life from the effects of pollution. Under the CWA, States and Indian
tribes are to establish water quality criteria to protect designated uses. State and Indian tribal
decision makers retain the discretion to adopt approaches on a case-by-case basis that differ
from this guidance when appropriate and scientifically defensible. While this manual
constitutes USEPA’s scientific recommendations regarding biological criteria to help protect
resource quality and aquatic life, it does not substitute for the CWA or USEPA’s regulations;
nor is it a regulation itself. Thus, it cannot impose legally binding requirements on USEPA,
States, Indian tribes or the regulated community, and might not apply to a particular situation
or circumstance. USEPA may change this guidance in the future.
This document has been approved for publication by the Office of Science and Technology,
Office of Water, U.S. Environmental Protection Agency. Mention of trade names, products, or
services does not convey and should not be interpreted as conveying, official USEPA approval,
endorsement or recommendation.
The suggested citation for this document is:
Gibson, G.R., M.L. Bowman, J. Gerritsen, and B.D. Snyder. 2000. Estuarine and Coastal Marine
Waters: Bioassessment and Biocriteria Technical Guidance. EPA 822-B-00-024. U.S.
Environmental Protection Agency, Office of Water, Washington, DC.
Acknowledgments
The authors wish to express their sincere appreciation to the Estuarine and Coastal
Marine Biocriteria Workgroup and the peer reviewers (Arthur Newell - NYDEC,
Judith Weis - Rutgers University, John Gentile - University of Miami, Edward Long -
NOAA, and Robert Diaz - Virginia Institute of Marine Science).
Estuarine and Coastal Marine Biocriteria Workgroup Attendees

1992 - 1997
(Long Term Participation)
Suzanne Bolton Cindy Driscoll

National Marine Fisheries Service MD Department of Natural Resources
(ST2) Oxford Laboratory
1315 East/West Hwy. 904 S. Morris St.
Silver Spring, MD 20910 Oxford, MD 21654
301-713-2363 410-226-0078
Michael L. Bowman Charles Eaton

Tetra Tech, Inc. Bio-Marine Enterprises
10045 Red Run Blvd. 2717 3rd Avenue North
Suite 110 Seattle, WA 98109
Owings Mills, MD 21117 206-282-4945
Dan Campbell Larry Eaton

c/o USEPA ERL/ORD NC Division of Water Quality
University of Rhode Island 4401 Reedy Creek Road
27 Tarzwell Drive Environmental Sciences Bldg.
Narragansett, RI 02882 Raleigh, NC 27607
919-733-6946
Dan Dauer
Department of Biology Douglas Farrell*
Old Dominion University FL Department of Environmental
Norfolk, VA 23529 Protection
804-683-3595 3804 Coconut Dr.
Tampa, FL 33619-8218
Robert Diaz
VA Institute of Marine Science Brigette Farren
Glouchester Point, VA 23062 USEPA, Region III
804-642-7364 1650 Arch Street
Philadelphia, PA 19103-2029
215-814-2767
Estuarine and Coastal Marine Waters: Bioassessment and Biocriteria Technical Guidance iii
Chris Faulkner Steve Jordan
USEPA, OWOW (4503F) MD Department of Natural Resources
1200 Pennsylvania Ave. 904 South Morris Street
Washington, DC 20460 Oxford, MD 21654
202-260-6228 410-226-0078
Jeroen Gerritsen Don Kelso

Tetra Tech, Inc. George Mason University
10045 Red Run Blvd. 3016 King Hall
Suite 110 4400 University Drive
Owings Mills, MD 21117 Fairfax, VA 22030
George Gibson, Jr. (4304) Steve Kent

USEPA FL Department of Environmental
Office of Water Protection
Office of Science and Technology 3319 Maguire Blvd.
1200 Pennsylvania Ave. Suite 232
Washington, DC 20460 Orlando, FL 32803
410-305-2618
Don Lear*
Steve Glomb Anne Arundel Community College
U.S. Fish and Wildlife Service 101 College Pkwy
4401 N Fairfax Dr. Arnold, MD 21012
Room 400 410-647-7100
Arlington, VA 22203
703-358-2201 Beth McGee
U.S. Fish and Wildlife Service
George Guillen Chesapeake Bay Field Office
TX Water Commission 1777 Admiral Cochrane Drive
District 7 Annapolis, MD 21401
5144 East Sam Houston Parkway, N 410-573-4524
Houston, TX 77015
713-457-5191 Margaret McGinty
MD Department of Natural Resources
Susan Jackson Tidewater Ecosystem Assessment
USEPA, OST/HECD (4304) Annapolis, MD 21401
1200 Pennsylvania Avenue, NW 410-260-8637
202-260-1800 Gil McRae
FL Marine Research Institute
100 Eighth Ave., SE
St. Petersburg, FL 33701
727-896-8626
727-823-0166 (fax)
iv Acknowledgements
William Muir Dave Russell
USEPA Region III USEPA Region III
1650 Arch Street (3ES41) Environmental Science Center
Philadelphia, PA 19107 701 Mapes Road
215-814-2541 Ft. Meade, MD 20755-5350
410-305-2656
Walt Nelson
USEPA Steve Wolfe
2111 SE Marine Science Dr. FL Department of Environmental
Newport, OR 97365-5260 Protection
541-867-4041 2600 Blair Stone Road
Tallahassee, FL 32399
Art Newell
NY Department of Environment
Division of Marine Resources
Building 40, SUNY
Stonybrook, NY 11790-235
516-444-0430
* Deceased
Acknowledgment:
Additional scientific, technical, editorial, and production contributions were made

by William Swietlik (USEPA), Laura Gabanski (USEPA), Jim Latimer (USEPA),
David Scott (Dalhousie University), Gail Chmura (McGill University), Zorana
Spasojeviz (McGill University), Jerome Diamond (Tetra Tech, Inc.), Abby Markowitz
(Tetra Tech, Inc.), Kristen Pavlik (Tetra Tech, Inc.), Brenda Fowler (Tetra Tech, Inc.),
Erik Leppo (Tetra Tech, Inc.), and Regina Scheibner (Tetra Tech, Inc.). This
document was prepared by Tetra Tech, Inc.
For the Ocean City/Bethany Beach case study in Section 13.6, thanks are given to
David Russell, USEPA Region III provided taxonomic identifications, William Muir,
USEPA Region III assisted with data gathering, Eileen Watts, USEPA Region III
provided data analysis. Jeroen Gerritsen, Tetra Tech, Inc. offered constructive
comments, and Kristen Pavlik, Tetra Tech, Inc. made final editorial changes. Their
essential contributions to this report are greatly appreciated.
Estuarine and Coastal Marine Waters: Bioassessment and Biocriteria Technical Guidance v
Estuarine and Coastal Marine Waters:
Bioassessment and Biocriteria Technical Guidance
CONTENTS
List of Figures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
List of Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xxi
Acronym List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xxv
Executive Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xxix
CHAPTER 1: Introduction: Bioassessment and Biocriteria . . . . . . . . . . . . . . . . . . . . . . 1-1

1.1 RATIONALE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
1.1.1 Water Quality Monitoring . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
1.1.2 Advantages of Bioassessment and Biocriteria . . . . . . . . . . . . . . . . . . . . . 1-1
1.2 LEGAL ORIGINS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
1.2.1 Clean Water Act . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
1.2.2 305(b) Reporting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
1.2.3 301(h) and 403(c) Programs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
1.2.4 304(a) Criteria Methodology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
1.2.5 Biocriteria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-5
1.3 USES OF BIOCRITERIA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-5
1.3.1 The Use of Bioassessment Data to Establish Biocriteria Appropriate
to Designated Beneficial Uses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-6
1.3.2 Expansion and Improvement of Water Quality Standards . . . . . . . . . . 1-9
1.3.3 Detection of Problems Other Methods May Miss or Underestimate . . 1-9
1.3.4 Helping the Water Resource Managers Set Priorities . . . . . . . . . . . . . . 1-9
1.3.5 Use of Biosurveys and Biocriteria to Evaluate the Success or Failure
of Management Initiatives or Regulations . . . . . . . . . . . . . . . . . . . . . . . . 1-9
1.4 PROGRAM INTERDEPENDENCE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-10
1.5 IMPLEMENTING BIOLOGICAL CRITERIA . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-10
1.6 CHARACTERISTICS OF EFFECTIVE BIOCRITERIA . . . . . . . . . . . . . . . . . . . . 1-11
1.7 CONCEPTUAL FRAMEWORK . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-11
1.7.1 Indicators of Biological Integrity and Survey Protocols . . . . . . . . . . . 1-12
1.7.2 Comparison to a Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-15
1.7.3 Assessment Tiers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-16
vii Contents
CONTENTS (CONTINUED)
CHAPTER 2: Biological Survey . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1

2.1 INDICATORS OF BIOLOGICAL INTEGRITY . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
2.2 PRIMARY MEASURES OF COMMUNITY CONDITION AND CHANGE . . . 2-1
2.2.1 Benthic Macroinvertebrates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
2.2.2 Fish . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
2.2.3 Aquatic Macrophytes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3
2.2.4 Phytoplankton . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-4
2.3 MEASURES OF COMMUNITY CONDITION AND CHANGE BEING
DEVELOPED . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-5
2.3.1 Zooplankton . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-5
2.3.2 Epibenthos . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-6
2.3.3 Paleoenvironmental Reconstruction: preserved remains . . . . . . . . . . . 2-7
2.4 THE USE OF INDEXES TO COMPILE AND EVALUATE
BIOLOGICAL DATA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-7
2.5 INDICATOR TAXA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9
CHAPTER 3: Habitat Characterization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1

3.1 FLOW AND HYDROGRAPHY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
3.1.1 Circulation and Tidal Regime . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
3.2 HABITAT TYPES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
3.2.1 Open Water . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
3.2.2 Soft Bottom Substrates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
3.2.3 Hard Bottom Substrates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
3.2.4 Aquatic Macrophytes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
3.2.5 Beaches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6
3.2.6 Sandflats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6
3.2.7 Mudflats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-7
3.2.8 Emergent Marshes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-7
3.2.9 Mangrove Forests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-7
3.3 WATER COLUMN CHARACTERISTICS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-7
3.3.1 Salinity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-9
3.3.2 Temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-10
3.3.3 Dissolved Oxygen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-10
3.3.4 pH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-12
3.3.5 Turbidity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-12
3.3.6 Nutrients . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-13
3.3.7 Contaminants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-14
3.3.8 Depth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-15
Estuarine and Coastal Marine Waters: Bioassessment and Biocriteria Technical Guidance viii
3.4 BOTTOM CHARACTERISTICS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-15

3.4.1 Sediment Grain Size . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-16
3.4.2 Total Organic Carbon, Total Volatile Solids, and Acid Volatile
Sulfides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-16
3.4.3 Sediment Oxidation-Reduction Potential . . . . . . . . . . . . . . . . . . . . . . . . 3-17
3.4.4 Sediment Contamination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-18
3.5 PROPOSED HABITAT PARAMETERS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-18
3.5.1 Tier 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-20
3.5.2 Tier 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-20
3.5.3 Tier 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-21
3.5.4 Tier 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-22
CHAPTER 4: Physical Classification and the Biological Reference Condition . . . . . . . 4-1

4.1 CLASSIFICATION APPROACH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1
4.2 PHYSICAL CLASSIFICATION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-4
4.2.1 Geographic Region . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-4
4.2.2 Estuarine Categories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-5
4.2.3 Watershed Characteristics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-6
4.2.4 Waterbody Characteristics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-6
4.3 ESTABLISHING BIOLOGICAL REFERENCE CONDITIONS . . . . . . . . . . . . . . 4-7
4.3.1 Historical Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-7
4.3.2 Reference Sites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-8
4.3.3 Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-9
4.3.4 Expert Opinion/Consensus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-10
4.4 USE OF REFERENCE SITES TO CHARACTERIZE
REFERENCE CONDITION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-11
4.4.1 Selected Reference Sites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-12
4.4.2 Reference Condition Derived From Population Distribution . . . . . . . 4-16
4.4.3 Site Specific Reference Sites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-17
CHAPTER 5: Sampling Program Issues, Biological Assemblages, and Design . . . . . . 5-1

5.1 ASSEMBLAGES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1
5.1.1 Benthic Macroinvertebrates (Infauna) . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
5.1.2 Fish . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-14
5.1.3 Aquatic Macrophytes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-15
5.1.4 Phytoplankton . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-16
5.1.5 Zooplankton (Developmental) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-18
ix Contents
5.1.6 Epibenthos (Developmental) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-19

5.1.7 Paleoenvironmental Systems (Developmental) . . . . . . . . . . . . . . . . . . . 5-20
5.2 SAMPLING DESIGN ISSUES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-21
5.2.1 Statement of the Problem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-23
5.2.2 Definition of the Assessment Unit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-24
5.2.3 Specifying the Population and Sample Unit . . . . . . . . . . . . . . . . . . . . . 5-24
5.2.4 Sources of Variability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-25
5.2.5 Alternative Sampling Designs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-27
5.2.6 Optimizing Sampling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-30
CHAPTER 6: Water Column & Bottom Characteristics . . . . . . . . . . . . . . . . . . . . . . . . . 6-1

6.1 SALINITY, TEMPERATURE, DISSOLVED OXYGEN & pH . . . . . . . . . . . . . . . 6-1
6.2 SECCHI DEPTH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1
6.3 DEPTH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1
6.4 SEDIMENT GRAIN SIZE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1
6.4.1 Estimation of “percent fines” (Tier 1) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1
6.4.2 Sediment Grain Size (Tiers 2 and 3) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4
6.5 RPD Layer Depth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-5
6.6 TOTAL VOLATILE SOLIDS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-5
6.7 SEDIMENT CONTAMINANT TOXICITY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-5
6.7.1 10-day Static Sediment Toxicity Tests with Marine and Estuarine
Amphipods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-5
6.7.2 10-day Static Sediment Toxicity Tests with Marine and Estuarine
Polychaetous Annelids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-6
6.7.3 Static Accute Toxicity Tests with Echinoid Embryos . . . . . . . . . . . . . . . 6-6
6.7.4 Toxicity Tests Using Marine Bivalves . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-7
6.8 NUTRIENTS (Tiers 2&3) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-7
6.9 TOTAL ORGANIC CARBON (Tiers 2&3) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-7
6.10 WATER COLUMN CONTAMINANTS (Tier 3) . . . . . . . . . . . . . . . . . . . . . . . . . . 6-8
6.11 ACID VOLATILE SULFIDES (Tier 3) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-8
6.12 SEDIMENT CONTAMINANTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-9
CHAPTER 7: Tier 0: Desktop Screening . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1

7.1 AREA AND GEOMORPHOMETRIC CLASSIFICATION . . . . . . . . . . . . . . . . . 7-1
7.2 HABITAT TYPE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2
7.3 WATERSHED LAND USE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2
7.4 POPULATION DENSITY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2
7.5 NPDES DISCHARGES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2
Estuarine and Coastal Marine Waters: Bioassessment and Biocriteria Technical Guidance x
7.6 BIOLOGICAL ASSEMBLAGES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2

7.7 WATER COLUMN AND BOTTOM CHARACTERISTICS . . . . . . . . . . . . . . . . . 7-3
CHAPTER 8: Tier 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-1

8.1 BENTHOS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-1
8.1.1 Sampling Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-3
8.1.2 Index Period . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-3
8.1.3 Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-3
8.2 FISH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-3
8.2.2 Sample Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-4
8.3 MACROPHYTES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-4
8.4 PHYTOPLANKTON . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-5
CHAPTER 9: Tier 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-1

9.1 BENTHOS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-1
9.1.2 Index Period . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-3
9.1.3 Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-3
9.2 FISH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-3
9.2.2 Sample Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-3
9.2.3 Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-3
9.3 MACROPHYTES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-3
9.3.2 Index Period . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-4
9.3.3 Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-4
9.4 PHYTOPLANKTON . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-4
9.4.2 Index Period . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-4
9.4.3 Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-5
9.5 EPIBENTHOS (Developmental) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-5
9.5.2 Index Period . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-5
9.5.3 Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-5
CHAPTER 10: Tier 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-1

10.1 BENTHOS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-1
xi Contents
10.1.1 Sampling Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-3

10.1.2 Index Period . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-3
10.1.3 Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-3
10.2 FISH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-3
10.2.2 Sample Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-3
10.2.3 Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-3
10.3 MACROPHYTES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-3
10.3.2 Index Period . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-4
10.3.3 Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-4
10.4 PHYTOPLANKTON . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-4
10.4.2 Index Period . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-4
10.4.3 Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-4
10.5 EPIBENTHOS (Developmental) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-4
10.5.2 Index Period . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-4
10.5.3 Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-4
10.6 ZOOPLANKTON (Developmental) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-4
10.6.2 Index Period . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-5
10.6.3 Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-5
10.7 PALEOENVIRONMENTAL SYSTEMS (Developmental) . . . . . . . . . . . . . . . . . 10-5
10.7.2 Sample Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-6
10.7.3 Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-6
CHAPTER 11: Index Development . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11-1

11.1 OVERVIEW . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11-1
11.2 CLASSIFICATION AND CHARACTERIZATION OF REFERENCE
CONDITION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11-2
11.2.1 Existing Classifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11-3
11.2.2 Assessing a priori Classifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11-6
11.3 INDEX DEVELOPMENT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11-6
11.3.1 Multimetric Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11-7
11.3.2 Discriminant Model Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11-13
11.3.3 Index Derived from Multivariate Ordination . . . . . . . . . . . . . . . . . . . 11-14
Estuarine and Coastal Marine Waters: Bioassessment and Biocriteria Technical Guidance xii
CHAPTER 12: Quality Assurance: Design, Precision, and Management . . . . . . . . . . . 12-1

12.1 PROGRAM DESIGN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12-1
12.1.1 Formulation of a Study Design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12-2
12.1.2 Establishment of Uncertainty Limits . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12-2
12.1.3 Optimizing the Study Design: Evaluation of Statistical Power . . . . . 12-3
12.2 MANAGEMENT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12-7
12.2.1 Personnel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12-7
12.2.2 Resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12-7
12.3 OPERATIONAL QUALITY CONTROL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12-7
12.3.1 Field Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12-8
12.3.2 Laboratory Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12-9
12.3.3 Data Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12-9
12.3.4 Reporting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12-9
CHAPTER 13: Case Studies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-1

13.1 PUGET SOUND - DEVELOPMENT OF TRAWL-BASED TOOLS FOR
THE ASSESSMENT OF DEMERSAL FAUNA (MACROINVERTEBRATES
AND FISHES): A PUGET SOUND PILOT STUDY . . . . . . . . . . . . . . . . . . . . . . . 13-1
13.1.1 Study Objectives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-1
13.1.2 Study Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-2
13.1.3 Study Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-3
13.2 GALVESTON BAY - DEVELOPMENT OF A RAPID BIOASSESSMENT
METHOD AND INDEX OF BIOTIC INTEGRITY FOR COASTAL
ENVIRONMENTS: NORTHWESTERN GULF OF MEXICO PILOT
STUDIES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-9
13.2.1 Study Objectives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-9
13.2.2 Study Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-9
13.2.3 Study Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-10
13.3 TAMPA BAY - DEVELOPMENT OF A COMMUNITY-BASED METRIC
FOR MARINE BENTHOS: A TAMPA BAY PILOT STUDY . . . . . . . . . . . . . . 13-21
13.3.1 Study Objectives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-21
13.3.2 Study Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-21
13.3.3 Study Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-23
13.4 NORTH CAROLINA - COMPARISON OF BIOLOGICAL METRICS
DERIVED FROM PONAR, EPIBENTHIC TRAWL, AND SWEEP NET
SAMPLES: A NORTH CAROLINA PILOT STUDY . . . . . . . . . . . . . . . . . . . . . 13-25
13.4.2 Study Location . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-25
xiii Contents
13.4.3 Study Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-25

13.4.4 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-27
13.4.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-30
13.5 INDIAN RIVER, FLORIDA - FIELD VERIFICATION OF MARINE
METRICS DEVELOPED FOR BENTHIC HABITATS: INDIAN RIVER
LAGOON, FLORIDA PILOT STUDIES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-33
13.5.2 Study Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-33
13.5.3 Study Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-33
13.6 OCEAN CITY, MD - BETHANY BEACH, DE - A PRELIMINARY STUDY
OF THE USE OF MARINE BIOCRITERIA SURVEY TECHNIQUES
TO EVALUATE THE EFFECTS OF OCEAN SEWAGE OUTFALLS
IN THE MID-ATLANTIC BIGHT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-39
13.6.2 Study Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-39
13.6.3 Study Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-42
13.6.4 Discussion and Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-43
13.6.5 Use of the Bethany Beach-Ocean City Data to Illustrate
Biocriteria Development . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-50
13.7 ENVIRONMENTAL QUALITY OF ESTUARIES OF THE CAROLINIAN
PROVINCE: 1995 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-55
13.7.1 Background/Objectives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-55
13.7.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-55
13.7.3 Benthic Infaunal Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-59
13.7.4 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-61
13.8 ASSESSMENT OF THE ECOLOGICAL CONDITION OF THE
DELAWARE AND MARYLAND COASTAL BAYS . . . . . . . . . . . . . . . . . . . . . 13-65
13.8.1 Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-65
13.8.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-65
13.8.3 Results/Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-69
Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . G-1
Literature Cited . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . L-1
Estuarine and Coastal Marine Waters: Bioassessment and Biocriteria Technical Guidance xiv
LIST OF FIGURES
Figure
1-1 Biocriteria for given classifications of estuaries and coastal marine areas . . . 1-8
1-2 Program interdependence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-10
1-3 The process for progressing from the classification of an estuary to

assessing the health of the estuary. Adapted from Paulsen et al. 1991 . . . . . 1-13
1-4 General comparison of Tiered Approach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-18
3-1 Chemicals measured in sediments by the EMAP-Estuaries program . . . . . . 3-19
4-1 Graphical representation of bioassessment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-3
4-2 Classification and assessment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-4
4-3 Biogeographical provinces. Adapted from Holland 1990 . . . . . . . . . . . . . . . . . 4-6
4-4 Estuarine and coastal marine biocriteria survey method useful for
stratified random (population distribution) reference site selection. Wet
season/high flow salinity pattern showing mainstem sampling sites for
four salinity and three substrate classifications . . . . . . . . . . . . . . . . . . . . . . . . . . 4-8
a priori reference site selection. Wet season/high flow salinity
pattern showing tributary reference sites and mainstem transects
for four salinity and three substrate classifications . . . . . . . . . . . . . . . . . . . . . . 4-14
4-6 Estuarine and coastal marine biocriteria survey method useful

for a prori reference site selection. Dry season/low flow salinity pattern
showing tributary reference sites and mainstem transects for four
salinity and three substrate classifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-15
xv Contents
LIST OF FIGURES (CONTINUED)
Figure
4-7 Hypothetical cumulative frequency distribution of metric values for all

sites in a given estuarine or coastal marine class. The dotted line
shows the metric value corresponding to the 95th percentile . . . . . . . . . . . . . 4-17
stratified random (population distribution) reference site selection. Dry
season/low flow salinity pattern showing mainstem sampling sites
for four salinity and three substrate classifications . . . . . . . . . . . . . . . . . . . . . . 4-18
4-9 Estuarine and coastal marine survey method for navigation channel
assessment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-20
marine site selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-20
5-1 Cross-section of sediment in clamshell bucket illustrating acceptable

and unacceptable grabs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-9
5-2 Description of various sampling methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-28
11-1 The process for progressing from the classification of an estuary to

assessing the health of the estuary. Adapted from Paulsen et al. 1991 . . . . . 11-3
11-2 Mean number of species and salinity at EMAP-Estuaries sampling

stations in the Virginian Province (from Weisberg et al. 1993) . . . . . . . . . . . . 11-4
11-3 Hypothetical box plot illustrating how a successful metric discriminates

between reference and stressed sites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11-9
11-4 Basis of metric scores using the 95th percentile as a standard . . . . . . . . . . . . 11-11
11-5 Steps 1-3. Establishing site scores on a contamination gradient . . . . . . . . . 11-16
11-6 Step 5. Abundance of species A and contamination scores. . . . . . . . . . . . . . 11-17
Estuarine and Coastal Marine Waters: Bioassessment and Biocriteria Technical Guidance xvi
Figure
12-1 Effect of increasing sample size from n1 to n2 on power . . . . . . . . . . . . . . . . . 12-4
12-2 Example sample size calculations for comparing proportions and

population means . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12-8
12-3 Six qualitative and quantitative data characteristics usually employed to

describe data quality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12-9
13-1 General location of the case studies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-2
13-2a Bony fish abundance and total fish abundance for reference and
contaminated sites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-4
13-2b Bony fish biomass and total fish biomass for reference and
contaminated sites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-4
13-2c Mean individual weights of fish species from contaminated and reference
stations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-5
13-3 Ponar samples: biotic index vs. salinity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-28
13-4 BI, total taxa and amphipod, and caridean taxa by salinity . . . . . . . . . . . . . 13-29
13-5 Development of biocriteria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-31
13-6 Bethany Beach - Ocean City study area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-40
13-7 Bethany Beach - Ocean City sampling locations . . . . . . . . . . . . . . . . . . . . . . . 13-41
13-8a Total number of macroinvertebrate individuals at Bethany Beach sites;

summer data, n=9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-44
xvii Contents
Figure
13-8b Total number of macroinvertebrate individuals at Ocean City sites;

summer data, n=9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-44
13-9a Total number of macroinvertebrate taxa at Bethany Beach sites;

summer data, n=9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-45
13-9b Total number of macroinvertebrate taxa at Ocean City sites; summer

data, n=9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-45
13-10a Simpson’s dominance index for macroinvertebrates at Bethany Beach

sites; summer data, n=9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-46
13-10b Simpson’s dominance index for macroinvertebrates at Ocean City sites;

summer data, n=9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-46
13-11a Shannon-Wiener diversity index for macroinvertebrates at Bethany

Beach sites; summer data, n=9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-47
13-11b Shannon-Wiener diversity index for macroinvertebrates at Ocean City

sites; summer data, n=9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-47
13-12a Richness index for macroinvertebrates at Bethany Beach sites;

summer data, n=9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-48
13-12b Richness index for macroinvertebrates at Ocean City sites; summer

data, n=9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-48
13-13 Proposed diagnostic nearfield station array . . . . . . . . . . . . . . . . . . . . . . . . . . 13-51
13-14 1995 Carolinian Province sampling stations . . . . . . . . . . . . . . . . . . . . . . . . . . 13-56
13-15 Frequency distribution of index scores for undegraded vs. degraded

stations in 1993/1995 “development” data set . . . . . . . . . . . . . . . . . . . . . . . . 13-62
Estuarine and Coastal Marine Waters: Bioassessment and Biocriteria Technical Guidance xviii
Figure
13-16 Comparison of the percent of expected bioeffects detected with the

benthic index vs. (A) four sediment bioassays and (B) three individual
infaunal attributes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-63
13-17 Percent area (and 95% C.I.) of CP estuaries with higher $ 1.5 to < 3),
and low (# 1.5) benthic index values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-64
13-18 Comparison of benthic index values by estuarine class and subregion . . . 13-64
xix Contents
Estuarine and Coastal Marine Waters: Bioassessment and Biocriteria Technical Guidance xx
LIST OF TABLES
Table
1-1 Applications of estuarine biological monitoring protocols and biocriteria . . . 1-3
1-2 Impacts on the marine environment of the Southern California Bight.

Modified from Bernstein et al. 1991 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-7
3-1 Habitat measurements for estuaries and coastal marine waters . . . . . . . . . . . 3-23
4-1 Comparison of elements for characterizing reference conditions (adapted

from Gerritsen et al. 1995) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-9
5-1 Potential benthic macroinvertebrate metrics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-3
5-2 Metrics from which the EMAP Virginian and Louisianian benthic indexes
were developed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-4
5-3 Sampling summary for infaunal benthic macroinvertebrates . . . . . . . . . . . . . . 5-5
5-4 Summary of bottom sampling equipment (adapted from USEPA 1992,

Klemm et al. 1992, and ASTM 1991) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-7
5-5 Mesh sizes used in estuary benthic monitoring programs . . . . . . . . . . . . . . . . 5-14
5-6 Sampling summary for fish . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-15
5-7 Potential aquatic macrophyte metrics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-17
5-8 Sampling summary for aquatic macrophytes . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-17
5-9 Sampling summary for phytoplankton . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-17
5-10 Sampling summary for epibenthos . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-20
5-11 Potential paleoecological indicators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-22
5-12 Sampling summary for paleoenvironmental systems . . . . . . . . . . . . . . . . . . . . 5-22
xxi Contents
LIST OF TABLES (CONTINUED)
Table
6-1 Water Column & Bottom Characteristics. “Addition” refers to added

detail or intensities for a parameters initiated in an earlier tier . . . . . . . . . . . . . 6-2
7-1 Tier 0 Desktop screening for estuaries and coastal marine waters . . . . . . . . . . 7-1
8-1 Tier 1 Assessment. Requires single field visit in spring or summer

index period . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-2
9-1 Tier 2 Assessment. Requires two or more field visits, one of which
should occur within chosen index period. In addition to requirements
from Tier 0 & 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-2
10-1 Tier 3 Assessment. Requires four or more field visits, one of which
should occur within the chosen index period. In addition to requirements
from Tiers 0-2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-2
11-1 Potential metrics for macrophytes, benthic macroinvertebrates, and fish

that could be considered for estuaries. Redundancy can be evaluated
during the calibration phase to eliminate overlapping metrics . . . . . . . . . . . . 11-8
11-2 Estuarine fish IBI metrics proposed by Thompson and Fitzhugh (1986) . . . 11-13
11-3 Maryland estuarine fish IBI metrics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11-14
12-1 Errors in hypothesis testing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12-4
12-2 Common values of (Z" + Z2$)2 for estimating sample size for use with
equations 1 and 2 (Snedecor and Cochran 1980) . . . . . . . . . . . . . . . . . . . . . . . . 12-6
12-3 Example QC elements for field and laboratory activities . . . . . . . . . . . . . . . . 12-10
13-1 A preliminary list of tolerant and sensitive fish and invertebrate species
from the Tacoma Waterways and Quartermaster Harbor . . . . . . . . . . . . . . . . 13-6
13-2 Candidate attributes of demersal fauna showing significant differences

in the present study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-7
Estuarine and Coastal Marine Waters: Bioassessment and Biocriteria Technical Guidance xxii
Table
13-3 Rationale for the inclusin of proposed nekton community metrics . . . . . . . . 13-12
13-4 Proposed seine metrics for use in an estuarine IBI along Texas coast . . . . . . 13-15
13-5 Proposed trawl metrics for use in an estuarine IBI along Texas coast . . . . . 13-16
13-6 Proposed gillnet metrics for use in estuarine IBI along Texas coast . . . . . . . 13-17
13-7 Proposed fish health index and condition factors for use in estuarine
rapid bioassessments of Texas Gulf coast tidal tributaries . . . . . . . . . . . . . . . 13-18
13-8 Advantages and disadvantages to using the epibenthic Renfro beam

trawl for the sampling of benthos . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-22
13-9 Farrell epifaunal index results for the Fort Desoto Park - Tampa Bay
Pilot Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-24
13-10 Advantages and disadvantages noted for the three benthic assemblage
collection methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-26
13-11 Functional metrics for the three benthic assemblage collection methods . . . 13-28
13-12 Comparison between winter and summer samples of the ability of the
various metrics tested to discriminate between impaired and low
impairment sites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-37
13-13 Establishment of reference condition using the mean of the interquartile

range of scores for three reference sites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-52
13-14 Comparison of the reference condition derived biocriteria to the

interquartile range of scores at the Bethany Beach and Ocean City
outfalls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-53
13-15 Estuarine resources of the Carolinian Province . . . . . . . . . . . . . . . . . . . . . . . . 13-57
13-16 Core environmental indicators for the Carolinian Province . . . . . . . . . . . . . . 13-58
xxiii Contents
Table
13-17 Exposure indicators under development in the Carolinian Province . . . . . . 13-59
13-18 Environmental parameters for the Maryland/Delaware Coastal Bays . . . . 13-68
13-19 Chesapeake Bay submerged aquatic vegetation habitat requirements

for a polyhaline environment (Dennison et al. 1993) . . . . . . . . . . . . . . . . . . . . 13-68
Estuarine and Coastal Marine Waters: Bioassessment and Biocriteria Technical Guidance xxiv
Acronym List
APHA American Public Health Association
AVS Acid Volatile Sulfides
BMP Best Management Practices
CCA Canonical Correspondence Analysis
CDF Cumulative Distribution Function
CSREES Cooperative State Research, Education, & Extension Service
CTD Conductivity - Temperature - Depth Meter
CV Coefficient of Variation
CWA Clean Water Act
DFA Discriminant Function Analysis
DGPS Differential Global Positioning System
DMRs Discharge Monitoring Reports
DNR Department of Natural Resources
DO Dissolved Oxygen
EMAP Environmental Monitoring & Assessment Program
EPA Environmental Protection Agency
ER-L Effects Range-Low
ER-M Effects Range-Median
FEI Farrell Epifaunal Index
FTE Full Time Equivalent
GIS Geographic Information System
GPS Global Positioning System
IBI Chesapeake Bay Estuarine Index of Biotic Integrity
ITI Infaunal Trophic Index
xxv Acronym List

MDS Multidimensional Scaling
NMDS Non-metric Multidimensional Scaling
NMFS National Marine Fisheries Service
NOAA National Oceanic and Atmospheric Administration
NODC National Oceanographic Data Center
NPDES National Pollutant Discharge Elimination System
NS&T National Status & Trends
PAHs Polyaromatic Hydrocarbons
PCA Principle Components Analysis
PCBs Polychlorinated Biphenyls
PCE Power Cost Efficiency
PCS Permit Compliance System
POTW Publically Owned Treatment Works
QA Quality Assurance
QC Quality Control
RBP Rapid Bioassessment Protocol
RPD Redox Potential Discontinuity
SAV Submerged Aquatic Vegetation
SEM Simultaniously Extracted Metals
SOP Standard Operating Procedure
SPM Suspended Particulate Matter
SQG Sediment Quality Guidelines
SQT Sediment Quality Triad
STORET STOrage & RETrieval
TDN Total Dissolved Nitrogen
TDP Total Dissolved Phosphorus
Estuarine and Coastal Marine Waters: Bioassessment and Biocriteria Technical Guidance xxvi
TMDL Total Maximum Daily Loads
TOC Total Organic Carbon
TPC Total Particulate Carbon
TPN Total Particulate Nitrogen
TPP Total Particulate Phosphorus
TSS Total Suspended Solids
TVS Total Volatile Sulfides
TWINSPAN Two-Way INdicator SPecies ANalysis
UPMGA Unweighted Pair Group Mean Averages
USDA CSREES United States Department of Agriculture Cooperative State

Research Education Extension Service
USGS United States Geological Survey
xxvii Acronym List

Executive Summary
This technical guidance document is in the study biogeographic region

based on the concept that bioassessment (USEPA 1996a)1
and biocriteria programs for estuaries
and near coastal waters are interrelated In water resource monitoring and
and critical components of protection, biological criteria are an
comprehensive water resource important addition to the traditional
protection and management. physical and chemical criteria used by
Understanding how estuarine EPA. The relative biological integrity, or
ecosystems function and respond to quality, of the resource can be assessed
human activity requires a holistic by comparing the health and diversity of
approach to protection and management its biological communities to the health
that integrates biological assessments and diversity of biological communities
into the more traditional chemical and in waters with the same physical
physical evaluations. Section 101 of the characteristics but which are relatively
Clean Water Act requires federal and unimpacted by human development .
state agencies to “restore and maintain There are basically four elements that
the chemical, physical, and biological comprise biocriteria:
integrity of the nation’s waters.”
Relatively undisturbed aquatic 1. Reference waters (relatively
ecosystems have high biological integrity, undisturbed areas that can be
defined as compared to study areas) serve
as “benchmarks” of water
the condition of an aquatic resource quality decision
community inhabiting unimpaired making.
waterbodies of a specified habitat as
measured by an evaluation of 2. The historical record of the
multiple attributes of the aquatic biological quality, diversity and
biota. Three critical components of productivity.
biological integrity are that the biota
is (1) the product of the evolutionary 3. Model projection of the
process for that locality, or site, (2) historical and reference
inclusive of a broad range of condition data (if necessary).
biological and ecological
characteristics such as taxonomic 4. The objective assessment of this
richness and composition, and information by a regional panel
trophic structure, and (3) is found of specialists such as state,
_________________
1
Biological criteria: Technical guidance for streams and small rivers. EPA 822-B-
96-001. U.S. Environmental Protection Agency, Office of Water, Washington, DC.
xxix Executive Summary

academic, and federal estuarine causes of degradation so that
ecologists, chemists, fisheries responsible management can be
biologists, oceanographers, and initiated.
resource managers.
This guidance provides detailed
The summation of these four factors is descriptions of the appropriate habitat
the biological criterion for a given measurements to make the subsequent
estuary or class of coastal water in a physical classification to be achieved.
geographic region. Examples of the The document then describes four levels
parameters included in a biocriterion are of investigative intensity or sampling
community measures or indexes drawn tiers. These tiers are suggested as one
from dynamic assessments of resident possible approach to organizing the data
fish, benthic invertebrate, macrophyte, gathering efforts and investigation
and planktonic assemblages making up needed to be able to establish biocriteria
the biological community. in a scientifically defensible manner.
Other approaches using variations of
Many natural resource agencies these tiers may be appropriate
throughout the United States have depending on program objectives.
begun the process of developing and
implementing bioassessments and < Tier 0 is a preliminary review of
criteria programs primarily for rivers existing literature and data available
and streams. This document is part of for the estuary or coastal water of
the effort to advance the use of these concern. It provides candidate
strategies with regard to estuaries and reference sites for the development
near coastal waters, thereby fostering of a reference condition;
the development of credible and
practical bioassessment programs. This < Tier I is a one-time site visit with
document is intended to provide preliminary data gathering to refine
managers and field biologists with the information in Tier 0 and
functional methods and approaches for establish candidate biocriteria;
bioassessment and biocriteria
development. < Tier II repeats and builds on
measurements initiated in Tier I and
In developing biological information, it establishes the reference condition
is imperative that the physical and data which is combined with the
chemical habitat be carefully measured historical record, possible models or
and documented. Information such as other extrapolations, and a
salinity, depth, sediment grain size, and consensus of regional expert opinion
water quality (including pH, to establish and employ the
temperature, DO, nutrients, and biocriteria for management decision
toxicants) is essential to proper making;
classification of the waters for
comparison and to the potential < Tier III is the diagnostic
subsequent investigation of possible investigation requiring the most
Estuarine and Coastal Marine Waters: Bioassessment and Biocriteria Technical Guidance xxx
sampling events and most extensive USEPA and the States and Tribes are
parameters to help establish better informed about the quality of our
management efforts for those waters nations extensive and coastal water
which do not meet the biocriteria. resources. The bioassessment/
biocriteria process is a particularly cost
Biocriteria development is not a one size effective screening tool to evaluate over
fits all proposition. Biocriteria can be all water quality and determine water
developed on biogeographical province resource status and trends. The
basis or on a smaller local basis to following table shows the progression of
account for the geographic, climatologic, the biocriteria process.
and biologic variation in the country.
Reference conditions and biocriteria
must be specific to each part of the
country in order to be responsive and
useful for decision making. It is
important to remember that such
circumstances vary and that this
document cannot address every
situation or experience. It is oriented
toward practical decision making rather
than research. Its primary audience is
intended to be state and tribal resource
managers. It is also intended to provide
managers and biologists with functional
methods and approaches to facilitate the
implementation of viable bioassessment
and biocriteria programs that meet their
individual needs and resources.
Biocriteria can be used to help support

and protect designated uses of water
resources; expand and improve water
quality standards; detect problems other
water quality measurements may miss
or underestimate; help water resource
managers set priorities for management
planning and, assess the relative success
or failure of management projects.
Biocriteria do not supersede or replace

physical or chemical criteria for water
resource decision making and
management. In fact biocriteria
augment these established measures so
xxxi Executive Summary

Sequential progression of the biocriteria process. Adapted from
Paulsen et al. 1991.
Preliminary Classification to Determine Reference Conditions and

Regional Ecological Expectations
Step 1 • Resource classification
• Determ ination of best representative sites (reference sites representative
of class categories)
Survey of Reference Sites and Selected Impaired Sites

• Collection of data on biota and physical habitat
Step 2
• Com pilation of raw data (taxonomic lists, abundance levels, and other
direct measures and observations)
Final Classification
Step 3 • Test preliminary classification
• Revise if necess ary
Metric Evaluation and Index Development

• Data analysis (data summ aries)
• Testing and validation of metrics by resource class
Step 4 • Evaluation of metrics for effectiveness in detecting impairment
• Selection of biological endpoints
• Aggregation of metrics into index.
• Te st the index for va lidity on ano ther d ata set.
Biocriteria Development
Step 5 • Adjustment by physical and chemical covariates
• Adjustment by designated aquatic life use
Implementation of Monitoring and Assessment Program

Step 6 • Determination of temporal variability of reference sites
• Identification of problems
Protective or Remedial Management Action

• Initiate program s to preserve ex ceptional waters
Step 7
• Implement managem ent practices to restore the biota of degraded
waters and to identify and address the causes of this degradation
Co ntin ual M on itorin g an d Periodic R eview of R eferences and Crite ria

• Biolog ical surveys con tinue to ass ess efficiency of m ana gem ent efforts
Step 8
• Evaluate poten tial changes in re ference condition and adjus t biocriteria
as managem ent is accomplished
Estuarine and Coastal Marine Waters: Bioassessment and Biocriteria Technical Guidance xxxii
Chapter 1
Introduction: Bioassessment
and Biocriteria
1.1 Rationale 1.1.2 Advantages of Bioassessment

and Biocriteria
1.1.1 Water Quality Monitoring
Bioassessment is intended to detect
The recognition that chemical water biological responses to pollution and
quality analyses do not adequately perturbation. Routine water quality
predict or reflect the condition of all monitoring for example, detects effects
aquatic resources has led to the of nutrient enrichment and chronic
development of measures of biological acidification, but normally is not
integrity expressed by biological criteria. designed to detect trace levels of
Biological surveys, criteria, and toxicants or contaminants, ephemeral
assessments complement physical and pollution events (e.g., acidic episodes,
chemical assessments of water quality by spills, short-lived toxicants and
reflecting the cumulative effects of pesticides, short-term sediment loading),
human activities, and natural or combined or synergistic impacts.
disturbances on a water body, including Bioassessment, by monitoring organisms
the possible causes of these effects. The that integrate the effects of
biological approach is best used for environmental changes, may in time
detecting generalized and non-specific detect these effects.
impairments to biological integrity, and
for assessing the severity of those Bioassessment, coupled with habitat
impairments. Then, chemical and assessment; i.e., physical and chemical
toxicity tests, and more refined habitat measurements, helps identify probable
assessments, can be used to identify causes of impairment not detected by
probable causes and their sources, and to physical and chemical water quality
suggest corrective measures. analyses alone, such as nonpoint source
pollution and contamination, erosion, or
For the purposes of bioassessment and poor land use practices. The detection
biocriteria development described here, of water resource impairment,
an estuary is a semi-enclosed water body accomplished by comparing biological
that has a free connection with the open assessment results to the biological
sea and an inflow of freshwater that criteria, leads to more definitive
mixes with the seawater; including chemical testing and investigations
fjords, bays, inlets, lagoons, and tidal which should reveal the cause of the
rivers. Coastal marine waters are those degradation. This, in turn, should
marine waters adjacent to and receiving prompt regulatory and other
estuarine discharges and extending management action to alleviate the
seaward over the continental shelf problem. Continued biological
and/or the edge of the U.S. territorial monitoring, with the data collected
sea. compared to the criteria, will determine
the relative success of the management
efforts.
Estuarine and Coastal Marine Waters: Bioassessment and Biocriteria Technical Guidance 1-1
1.2 Legal Origins 1.2.3 301(h) and 403(c) Programs
1.2.1 Clean Water Act Two other programs within USEPA that
specifically rely on biological
The CWA, Section 101, requires federal monitoring data in coastal marine areas
and state governments to "restore and are the §301(h) Waiver Program and the
maintain the chemical, physical, and §403(c) Ocean Discharger Program. The
biological integrity of the nation's §301(h) program allows estuarine and
waters." Thus, the Act mandates the marine dischargers who meet specific
restoration and maintenance of criteria set forth by USEPA to defer
biological integrity in the Nation's secondary treatment if they can show
waters. The combination of performing that their discharge does not produce
biological assessments and comparing adverse effects on resident biological
the results with established biological communities. As part of the modified
criteria is an efficient approach for NPDES permit received through this
evaluating the biological integrity of waiver program, the dischargers are
aquatic ecosystems. Other pertinent required to conduct extensive biological
sections of the CWA are Sections 305(b), monitoring programs designed to detect
301(h), and 403(c). Table 1-1 outlines detrimental effects to those biological
suggestions for the application of communities.
biological monitoring and biocriteria for
estuaries through existing state programs The §403(c) Ocean Discharge Program
and regulations. requires that all dischargers to marine
waters provide an assessment of
1.2.2 305(b) Reporting discharge impact on the biological
community in the area of the discharge
States and the USEPA report on the and on the surrounding biological
status and progress of water pollution communities. This program requires
control efforts in §305(b) reports extensive biological monitoring for some
submitted every two years. Inclusion of dischargers. Community bioassessment
biological assessment results in these methods are valuable in this program
reports will improve the public for trend assessment and, in some cases,
understanding of the biological health refinement into more rigorous and
and integrity of water bodies. Many of definitive assessments.
the better known and widely reported
recoveries from pollution have involved 1.2.4 304(a) Criteria Methodology
the renewal or reappearance of valued
species to systems from which they had This technical guidance was developed
nearly disappeared, or the recovery of a under the §304(a) requirement that,
viable fishery from contaminants. “criteria for water quality accurately
Examples of such recoveries are the reflecting the latest scientific knowledge
restoration of the lower Potomac River of the kind and extent of all identifiable
and of shellfish beds in Maine. effects on health and welfare including,
Incorporation of biological integrity in but not limited to, plankton, fish,
§305(b) reports will ensure the inclusion shellfish, wildlife, plant life, shorelines,
of a bioassessment endpoint, and will beaches, aesthetics, and recreation
make the reports more accessible and which may be expected from the
meaningful to many segments of the presence of pollutants in any body of
public.
1-2 Introduction - Bioassessment & Biocriteria

water . . .” be published and updated as and biological integrity of navigable and
needed. ground waters, waters of the contiguous
zone, and the ocean. This also covers
Under this section, a guidance document information identifying conventional
must include information on restoration pollutants, such as those classified as
and maintenance of chemical, physical, biological oxygen demanding,
Ta ble 1 -1. Applications of estuarine biological monitoring protocols and biocriteria.
Program Biological Monitoring and Bio log ical C riteria

Assessment
Section 305(b)/ • Improving data for beneficial use • Identifying waters that are
Reporting ass ess m ent. not ac hieving their aquatic
• Improving water quality reporting. life use sup port.
• Defining an understa ndable
endpoint in terms of
“biological health” or
“biological integrity” of
wate rbod ies."
National Estuary • Assessing status of biological • Identifying estuaries that are
Program (NEP) components of estuarine systems. not attaining designated use
• Develop monitoring objectives and (including aquatic life use)
performance criteria. sup port.
• Establish testable hypothesis and • Defining estuarine biological
select statistical methods. integrity based on a
• Assessing estuarine trophic status reference condition.
and trends, and assessing • Identifying impairments due
biological trends. to toxic substances,
• Select analytical methods & eutrophication, and habitat
alternative sampling designs. modification.
• Evaluate expected monitoring study
performance.
• Im plem ent m onitoring stu dy & data
analysis. [Monitoring and sampling
needs vary for each estua ry]
Section • Eva luating non point source impac ts • Determining effectiveness of

319/Nonpoint and sources. nonpoint source controls.
Source Program • Measuring site-specific ecosystem
response to remediation or
mitigation activities.
• Assessing biological resource
trends within watersheds.
W atershed • Assessing biological resource • Setting goals for watershed
Protection trends within watersheds. and regional planning.
Approach
TMD Ls • Identifying biological assemblage • Identifying water
and habitat impairments that quality-limited waters that
indicate nonattainment of water require TMDLs.
quality standards. • Establishing endpoints for
• Priority ranking waterbodies. TM DL developm ent, i.e.,
• Docum enting ecological/water measuring success.
quality response as a result of
TMD L implementation.
Ta ble 1 -1 (con t’d). Applications of estuarine biological monitoring protocols and biocriteria.
Program Biological Monitoring and Bio log ical C riteria
Assessment
NPDES P ermitting • Measuring improvem ent or lack of • Performing aquatic life use
improvement of mitigation efforts. compliance monitoring.
• Developing protocols that • Helping to verify that
demonstrate the relationship of NPD ES pe rm it limits are
biological metrics to effluent resulting in achievement of
characteristics. state water quality standard.
State Monitoring • Improving water quality reporting. • Providing a benchmark for
Programs • Docum enting improvement or lack measuring effectiveness of
of im prov em ent of m itigation efforts controls and performing
including estuary clean-up efforts, watershed/regional
TMD L application, NPDES efforts, planning.
nonpoint source pollution controls,
etc.
• Problem identification and trend
ass ess m ent.
• Prioritizing waterbodies.
Risk Assessment • Providing d ata need ed to estim ate • Providing an assessment or
ecological risk to assessment m eas urem ent endp oint.
endpoints.
W ater Q uality • Developing data bases for estuarine • Providing benchmark for
Criteria and phytoplankton, macroinvertebrates, identifying waterbodies that
Standards fish, plants, and other are not attaining aquatic life
assemblages. use classification.
• Developing indices that assess • Developing site-specific
estuarine biota compared to a standards.
reference.
• Providing data for aquatic life use
classifications.
Section 301(h)/ C Allows marine discharges who meet C Providing threshold against
W aiver Program USE PA criteria to defer seconda ry which to m easure
treatment if discharge does not detrimental effects on
produce adverse effects on resident biological comm unities.
biological comm unities.
Section C Re quires m arine discharg ers to C Providing threshold against
403(c)/Ocean provide an assessment of which to m easure
Discharge Program discharge impact on biological discharger impacts on
comm unity in discharge area as biological comm unities.
well as surrounding comm unities.
Section 304(a)/ C Provides information on restoration C Providing the benchmark for

Criteria and m ainten ance of c hem ical, measuring the effects of
Methodology physical, and biological integrity of pollutants on the biological
waters. com m unity.
C Identifies conventional pollutants,
their concentrations and effects on
surrounding comm unities.

suspended solids, fecal coliform, and pH. instances, “minimally impaired” sites
Section 304(a)(8) authorizes USEPA to are not available because the entire area
develop and publish methods for has been degraded. Biocriteria are then
establishing and measuring water based on historical data, empirical
quality criteria for toxic pollution, on models if appropriate, and expert
other bases than a pollutant by pollutant judgement to set a condition better than
approach. This includes biological present sites. Restoration of the
monitoring and assessment methods. degraded area must therefore be
Specific states have the authority to accomplished before any such reference
enforce more stringent regulations as sites can be established.
necessary.
Biological criteria typically include the
1.2.5 Biocriteria condition of aquatic communities at
designated reference sites as an
A major purpose of developing important component. The conditions
biological assessment methods is to of aquatic life found at these sites are
establish biological criteria for surface used to help detect both the causes and
waters. Biological criteria are guidelines levels of risk to biological integrity at
or benchmarks adopted by states to other sites of that type in a region. In
evaluate the relative biological integrity keeping with the policy of not
of surface waters. The criteria are degrading the resource, the reference
defined as "narrative expressions or conditions—like the criteria they help
numerical values that describe the define—are expected to be upgraded
biological integrity of aquatic with each improvement to the water
communities inhabiting waters of a resource. It is important that biological
given designated aquatic life use" criteria not be based on data derived
(USEPA 1990). Biological criteria are, in from degraded reference sites. In fact, a
effect, a practical approach to concerted effort should be made by
establishing management goals designed States and other jurisdictions to preserve
to protect or restore biological integrity. the quality of designated reference sites
Biocriteria can be adopted by a State into by setting those areas aside in preserves
their water quality standards, along with or parks or by inclusion in use
chemical, physical and toxicity criteria to protection programs so that continuity
better protect aquatic life uses of of the biocriteria data base can be
waterbodies. maintained. Biocriteria supported by
bioassessment surveys serve several
Biocriteria can be developed from purposes in surface water programs,
reasonable expectations for the locality discussed in the following section.
based on: historical data; reference
conditions; empirical models; and the 1.3 Uses of Biocriteria
consensus judgment of regional experts
(Section 1.4.2). The reference condition The biocriteria-bioassessment process
component of biocriteria requires helps resource managers identify
minimally impaired reference sites impairment of designated beneficial
against which the study area may be uses. It expands and improves
compared. Minimally impaired sites are designated beneficial use classifications
not necessarily pristine; they must, and their associated water quality
however, exhibit minimal influence by standards. It detects problems other
human activities relative to the overall
region of study (USEPA 1996a). In some
survey methods may miss or process and usually is presented in a
underestimate. It is a process which comprehensive index of many biological
helps the resource manager set program characteristics such as an IBI or the
priorities. It can also be used to evaluate EMAP benthic index (Chapter 11).
management and regulatory efforts. For
example, the information summarized in The horizontal axis represents a
Table 1-2 indicates that wastewater progression of socially determined use
outfalls are a controlling factor of soft designations; i.e., those predominant
bottom benthic communities and that uses the State has concluded are
there is a moderate scientific appropriate for a particular estuary,
understanding of the effects of these region or area within the class. These
outfalls specifically in the Southern hypothetical designated uses are
California Bight (USEPA 1992). arranged on the graph from those
usually associated with relatively low
1.3.1 The Use of Bioassessment Data water resource quality on the left, to
to Establish Biocriteria those associated with very high,
Appropriate to Designated relatively natural, resource quality on
Beneficial Uses the far right.
The hypothetical information presented The potentially optimal array of

in Figure 1-1 represents data collected for biological criteria for this class of
a given class of similar estuarine or waters, then, are scores between the
coastal reaches (e.g., similar sediments, reference condition and the level of
depths, and salinities) within the same biological integrity; i.e., between that
geographic region. For these areas some which is achievable and that which is
high level of resource quality can be ideal. The narrower this area, the higher
conceived which represents a pristine the quality of the waters throughout the
condition, essentially the optimum class, and the less restoration
potential or integrity of those waters. A management is required. The objective,
completely unimpaired (no negative then, is to protect these resources.
human impacts upon the organisms of
the natural system) estuary or coastal On the same horizontal axis, a class of
marine area is referred to as having high quality regional uses are further
biological integrity. The approximation described by a subset of aquatic life
of this ideal quality at the top of a uses. These are the designated uses for
continuum can be expressed by a variety which management goals are also
of environmental measures of the biota described by desirable characteristics of
indicated on the vertical axis of the the aquatic biota to be especially
graph. The determined ideal level of protected, such as “protection of the
biological measurements at the health and diversity, undiminished, of
maximum score is shown by the upper all indigenous species of fish and
horizontal line (equivalent to biological invertebrates” for those designated as
integrity). A second horizontal line exceptional natural waters. Resource
somewhat below this is the level set as managers need to apply their first,
the reference condition, the attainable concerted efforts to those uses because it
level of integrity derived from actual is usually more cost-effective and
measurements from among the highest resource-conservative to protect existing
quality areas in the class. All high quality areas than it is to restore
information on this axis is expected to be degraded ones.
objectively derived through the scientific

Table 1-2. Impacts on the marine environment of the Southern California Bight. Modified from
Bernstein et al. 1991.
Valued Ecosystem Components
Hard Bottom Benthos
Wetlands & Estuaries

Commercial Shellfish
Soft Bottom Benthos
Fish Eggs & Larvae

Marine Mammals
Phytoplankton
Demersal Fish
Human Health
Zooplankton
Marine Birds
Pelagic Fish
Kelp Beds
Intertidal
Sources of
All
Perturbation
Storms
El Ninos
˜
California Current
Upwelling
Net effect of each source on all components

Blooms/Invasions
Ecol. Interactions
Power Plants
Wastewater Outfalls
Dredging
Rivers/Storm Runoff
Commercial Fishing
Sport Fishing
Habitat Loss/Mod.
Oil Spills
Net effect of each source on all components
All
KEY
Potential Importance Understanding
Controlling Moderate High
Moderate
Major Some Low
Figure 1-1
Biocriteria for
given
classifications of
estuaries and
+,*+
coastal marine
areas. Shaded %LRORJLFDO ,QWHJULW\
boxes represent
the appropriate
%LRORJLFDO 0HDVXUHPHQWV 6FLHQWLILF

biocriterion range
for selected
classes.
5DQJH RI %LRORJLFDO &ULWHULD
Unshaded boxes 0HHWV
represent the
0HHWV RU ([FHHGV
range of
measurement 5HIHUHQFH &RQGLWLRQ
results for test %LRFULWHULRQ 6'
sites in given
)DLOV
classes. The
vertical arrows
above the boxes ,QWHULP
for the %LRFULW
“significantly 6LJQLILFDQWO\ 7UHDWHG

$OWHUHG (VWXDULHV 'LVFKDUJHV WR
altered estuaries
DQG &RDVWDO (VWXDULHV DQG 3URWHFWHG IRU ([FHSWLRQDO
and coastal marine 0DULQH $UHDV &RDVWDO 0DULQH 3DUWLFXODU 1DWXUDO
areas” class /2: +DUERU 6KLSSLQJ &KDQQHO $UHDV )LVKHULHV (VWXDULHV
indicate the goal of

raising the 27+(5 '(6,*1$7(' 86(6 $48$7,& /,)( 86(6 +,*+
biocriterion for
these waters over '(6,*1$7(' 86(6 62&,$/
time in response to
restoration efforts.
for similar areas of the region. An

interim biocriterion for these areas may
Selected biocriteria with an acceptable be set with the intention of progressively
range of variation, perhaps one standard raising the criterion when sequential
deviation, are shown as cross hatched restoration efforts are accomplished
boxes appropriately located for each through a long range management
designated use. Test results for a given effort.
area in any use classification (“box and
whisker” plots showin g the full range of The “other desi gnated uses” to the left
measurements including variation for of the bifurcation line may still be
that area) can then be compared surveyed to assist management decision
graphically to the biocriterion for that makers; however, they fail to meet the
designated use. Three interpretations of criteria, and there are no designated
an estuarine or coastal marine area meets aquatic life uses which apply.
its criterion, meets or perhaps even
exceeds its criterion, and fails to meet the The designated uses, aquatic life uses
criterion are illustrated. and biocriteria are all hypothetical in
this illustration, but the
A fourth possible result is the marginal interrelationships of societal and
condition of significantly altered systems scientific elements of decision making
such as urban harbors or shipping should be evident. They are
channels. The original condition of these independent processes linked by an
areas may very well have been within environmental ethic and the USEPA
the optimal range of biotic health and policy of antidegradation of water
diversity for the region, but intense resource quality (the reference condition
development has significantly altered “bottom line” so to speak). A rational
them so that as a group they no longer decision can be made which balances
meet the minimum reference condition that which is ideal with that which is

achievable measured by the objective impaired, and those in good condition
processes of science. for which protection rather than
remediation is required, can all be
1.3.2 Expansion and Improvement of identified. Rational decisions can then
Water Quality Standards be made about how to apply limited
resources for the best results in
When a State adopts biological criteria in accordance with the needs and priorities
their water quality standards to protect of the state.
aquatic life uses, the criteria become
benchmarks for decision making, and 1.3.5 Use of Biosurveys and
may form the basis for requirements in Biocriteria to Evaluate the
NPDES permits and other regulatory Success or Failure of
programs. Management Initiatives or
Regulations
1.3.3 Detection of Problems Other
Methods May Miss or The manager may design a biosurvey to
Underestimate collect data before and after a permit,
regulation or other management effort
In the process of establishing biocriteria, has been implemented, perhaps
more data and information is inevitably augmented by spatially distributed
developed than was previously nearfield/farfield sampling as well.
available. The review of this new With this information and the biocriteria
information often reveals problems not decision making benchmark, it is
evident before or provides expanded possible to clearly evaluate the
insight into existing concerns and issues. environmental response of the system to
Armed with this information, a water the methods applied. This is useful in
resources manager is better able to the NPDES permit review process as a
examine issues and make decisions. way to help determine the effectiveness
of permit controls. Typically, biocriteria
1.3.4 Helping the Water Resource are not used directly in NPDES permits
Manager Set Priorities as effluent limitations. Biomonitoring
above and below a permit site when
In light of the new information described compared to the established biocriteria
above, the schedule of activities, will reveal the adequacy of the permit to
allocation of funds, and uses of achieve its intended purpose.
personnel and equipment may be more
appropriately prioritized according to If the biota are unimpaired or
the urgency or magnitude of the recovering, it may be wise to leave the
problems identified. permit, management practice or
regulation as is. If the biota are
With the expanded available biological impaired or declining, the review
information augmenting chemical and recommendation may be to change the
physical information, managers can permit, management technique or
apply a triage approach to water regulation accordingly. With NPDES
resource projects based on the actual permits, the five year review cycle
condition of the biota affected. This is allows sufficient time for extensive
much like a physician evaluating biological information to be developed
multiple emergency medical patients. so this determination can be made with
Essentially, areas that are critically reasonable confidence.
impaired, those that are moderately
1.4 Program Interdependence elements which are described in the
biological criteria technical guidance
It should be readily evident from the documents such as this one:
applications described above that
physical, chemical, and biological < Bioassessment Protocols are
surveys and monitoring (repetitive methods used to assess the status
surveys of the same area) and biological and trends of water bodies.
criteria are interrelated in the water Guidance documents for
resource management process. Figure 1-2 bioassessment contain suggested
illustrates this interrelationship, often methods and protocols for
referred to as “adaptive management.” establishing monitoring programs
In this continually cycling process, that use biological assessment.
monitoring provides the information
necessary to identify problems and to < Biocriteria Guidance assists states
establish biocriteria for the decision in establishing biological criteria for
making, management planning, and water bodies. Biocriteria are a series
implementation necessary to respond of ambient water resource quality
appropriately. Continued monitoring values or statements of condition
then reveals the relative success of the that relate to the desired biological
effort by comparing the new results to integrity for that class of waters.
those criteria again. At this point the When established they can be used
criteria or the management plan may be to evaluate similar water bodies in
adjusted as needed and the cycle repeats. that region. Implementation of
Ideally, the estuarine or coastal biocriteria requires use of
waters improve with each cycle. bioassessment protocols and a state
or regional biomonitoring database.
The National Program Guidance for
Figure 1-2 biocriteria describes issues related to
Program
Interdependence
development and implementation
(USEPA 1990). The first biocriteria
technical guidance issued was for
streams and small rivers (USEPA
1996a). It incorporated both
biosurvey techniques and biocriteria
development methods. It was
followed by the Lakes and Reservoir
Bioassessment and Biocriteria
Guidance (USEPA 1998). Each of
these documents incorporated
biosurvey techniques and the same
approach is being followed in
similar documents for rivers,
1.5 Implementing Biological wetlands, and coral reefs in addition
Criteria to this present technical guidance
for estuaries and coastal marine
Implementing biocriteria requires an waters.
established and standardized
methodology for biological assessment
adjusted to regional or state conditions.
Hence, guidance for state and regional
development of biocriteria has two

1.6 Characteristics of degradation, and stimulate restoration
of degraded sites.
Effective Biocriteria
Generally, effective biocriteria share Developing and implementing

several common characteristics: biological criteria occurs in three steps
(USEPA 1996a):
< Provide for scientifically sound, cost-
effective evaluations; 1. Planning the biocriteria
development program, including:
< Protect sensitive biological values;
C definition of program objectives;
< Protect healthy, natural aquatic C establishment of interagency
communities; cooperation;
C identifying acceptable levels of
< Support and strive for protection of uncertainty for decisions made
chemical, physical, and biological on the basis of biocriteria;
integrity; C establishing data quality
objectives.
< May include specific characteristics
required for attainment of 2. Characterizing reference conditions
designated use; for biocriteria and identifying
candidate reference sites, which may
< Are clearly written and easily require a biological survey.
understood;
3. Establishing biocriteria based, in
< Adhere to the philosophy and policy part, on characterized reference
of nondegradation of water resource conditions and designated use
quality; classes of the state.
< Are defensible in a court of law. 1.7 Conceptual Framework
In addition, effective biocriteria are set at The central principle of biological

levels sensitive to anthropogenic assessment is comparison of the
impacts; they are not set so high that biological resources of a water body to a
sites that have reached their full biological criterion based, in part, on a
potential are considered as failing to reference condition. Impairment of the
meet the criterion, nor so low that water body is judged by its departure
unacceptably impaired sites are rated as from the biocriteria. This approach
meeting them, which defeats the purpose presumes that the purpose of
of the CWA. The establishment of management is to prevent and repair
formal biocriteria warrants careful anthropogenic; i.e., human-induced,
consideration of planning, management, damage to natural resources. Biological
and regulatory goals and the best assessment of water bodies is predicated
attainable condition at a site. Balanced on our ability to define, measure, and
biocriteria will allow multiple uses to be compare biological integrity between
considered so that any conflicting uses similar systems. This requires an
are evaluated at the outset. The best
balance is achieved by developing
biocriteria that closely represent the
natural biota, protect against further
operational definition of biological development of multivariate models:
integrity as follows:
< Comparison of indicator values —
“...the condition of the aquatic Indicator of metric values can be
community inhabiting compared directly to the reference
unimpaired water bodies of a condition, without development of
specified habitat as measured by an index. This has been used most
community structure and often for paleoecological
function (USEPA 1990).” comparison, where biological
indicators are limited to certain
The functional definition also requires indicator species, deposition rates,
definitions of "unimpaired" and organic carbon loss, etc. (Turner and
"community structure and function", and Rabalais 1994, Sen Gupta et al. 1996,
the habitat must be specified. Cooper and Brush 1991, Latimer et
Community structure and function is al. 1997).
operationally defined by the biological
measures chosen for bioassessment, < Multimetric index — The
consisting primarily of measures of multimetric approach is to define an
species richness, trophic diversity array of metrics or measures that
(relative numbers of herbivores and top individually provide limited
carnivores), and indicator species. In information on biological status, but
addition to biological community when integrated, function as an
structure and function, chemical (DO, overall indicator of biological
salinity, contaminants, dissolved TOC, condition. Metrics incorporate
inorganic nitrogen, etc.) and physical information from individual,
(sediment composition) attributes are population, and community levels
measured to define an unimpaired site. into a single, ecologically-based
The combined attributes form the basis index of water resource quality
for defining reference conditions for (Gray 1989, Plafkin et al. 1989, Karr
biological criteria. When unimpaired 1991). The index is typically a sum
water bodies do not exist within a or an average of standardized scores
region, an operational definition of of its component metrics (Barbour et
unimpaired can be developed from a al. 1999). Developed initially for
combination of minimally impaired streams, the multimetric approach
estuaries and coastal waters, historical has increasingly been applied to
information, and professional judgment estuaries (Weisberg 1997, Hyland et
(Section 1.7.2). Figure 1-3 shows a al. 1998).
simplified framework for progressing
from an estuarine classification to < Discriminant analysis to develop an
assessing the health of the estuary. index from metric values — In this
approach, metrics (calculated as
1.7.1 Indicators of Biological above) are used to develop a
Integrity and Survey Protocols multivariate discriminant analysis
model to distinguish reference sites
Several analytical approaches have been from impaired sites. The calibrated
developed to assess the biological model is then applied to assessment
condition of waterbodies within the sites to determine whether they are
framework of comparison to reference, impaired. This approach was used
ranging in complexity from simple in EMAP-Near Coastal for the
comparison of indicator values, to

Figure 1-3
The process
Estuarine Class for progressing
Designation from the
classification
Tier 0 of an estuary
Historical Data to assessing
Review the health of
the estuary.
Tier 1 Tier 2 Tier 3 Adapted from
Sampling Sampling Sampling Paulsen et al.
1991.
Evaluation and
Calibration of Metrics
and other Indicators
Aggregation
Biocriteria
Relative to
Estuary Class
Assessment
of Sites
Virginian and Gulf provinces (Paul approach is highlighted in this

et al. 1999, Engle et al. 1999). guidance. This is because it is the best
developed and most extensively used
Multivariate ordination method to date. Investigators should
approaches — Several approaches carefully consider what is most
have been developed using appropriate for their specific program.
multivariate ordination to examine Time and experience will ultimately
differences in species composition determine the best approach or
between reference and impaired combination for each state to use.
sites. The purpose of ordination Chapter 11 goes into further detail about
analysis is to reduce the complexity methods of classification and assessment
of many variables (for example, using all three approaches.
abundances of over 100 species from
many estuarine sites), by re-ordering The multimetric concept came to fruition
the information into fewer variables. with the fish Index of Biotic Integrity
These approaches have been used to (IBI) first conceived by Karr (1981). The
show the effects of oil drilling in the IBI aggregates various elements and
North Sea (Warwick and Clarke surrogate measures of process into a
1991), and to develop an index of single assessment of biological
benthic quality in California (Smith condition. Karr (1981) and Karr et al.
et al. 2000). (1986) demonstrated that combinations
of these attributes or metrics provide
While all of these approaches are valuable synthetic assessments of the
appropriate to biocriteria development status of water resources.
when properly applied, the multimetric
A metric is a calculated term or possible stress from anthropogenic
enumeration representing some aspect of sources;
biological assemblage structure,
function, or other measurable < Community structure and
characteristic. Similarly, each of the composition, or the number and
assemblages (e.g., fish, benthic kinds of species in an assemblage.
macroinvertebrates composing the Exotic species are typically
aquatic community) measured would be undesirable, and high diversity is
expected to have a response range to usually desirable. Species structure
perturbation events or degraded metrics include diversity and
conditions. Thus, biosurveys targeting evenness indexes as well as presence
multiple species and assemblages; i.e., of indicator species, counts of
multimetric, will likely provide detection tolerant or intolerant species, the
capability over a broad range of impacts, percentage of individual taxa in
and the biocriteria derived from their comparison to the total number
results could provide protection to a sampled, and abundance
large segment of the ecosystem. proportions of taxonomic groups
(e.g. crustaceans, mollusks,
Metrics can be expressed numerically as polychaetes), or comparisons of
integers or ratios. Consistent routines in infauna vs. epifauna;
normalizing individual metric values
provide a means of combining metric < Trophic structure, or the relative
scores which initially consisted of proportion of different trophic levels
dissimilar numerical expressions. and functional feeding groups (e.g.,
However, final decisions on impact/no Barbour et al. 1992). In estuaries,
impact or management actions are not abundant, diverse, and relatively
made on the single, aggregated value large top carnivores (e.g.,
alone. Rather, if comparisons to piscivorous fish) are typically
established reference values indicate an desirable as representative of a
impairment in biological condition, broad, stable, and substantial
component parameters (or metrics) are trophic network;
examined for their individual effects on
the aggregated value and for indications < System function, or the
of potential causes. productivity and material cycling of
the system or its components
Assessment of biological integrity using (trophic levels, assemblages,
this multimetric approach typically species). Measures of system
focuses on four broad classes of function include primary
community properties. Ecological production and standing stock
systems respond to anthropogenic biomass.
impacts with changes in one or more of
these classes of properties (e.g., Karr et Since biological integrity is defined as an
al. 1986, Schindler 1988, Plafkin et al. indicator of undisturbed conditions, it
1989, Schindler et al. 1989, Karr 1991, too must be measured relative to those
Barbour et al. 1992). The four properties conditions. The requirement of the
are: biological criteria process for a reference
by which to measure biological integrity
< Health of populations, typically makes it a practical tool (sensu Peters
expressed as number of individuals 1991) for managing society's impact on
per m2 or as biomass, reflecting the natural environment.

Monitoring and assessment programs < Cost-effective Cost of a metric
typically do not have the resources to should be proportional to the value
measure all ecological attributes of of the information obtained.
concern to the public and to managers, Usually, the simplest approach is
and assessment tools must be cost- most cost-effective and should be
effective. Ideally, metrics selected for selected so long as results are
monitoring must be scientifically valid; sufficient to the agency's objectives;
should not require large amounts of
expensive equipment; and should be < Environmentally Benign to
relatively rapid in the field. The selected Measure Sampling methods that
variables must be: significantly disturb or alter habitats
and biota should be avoided.
< Related to Biological Integrity In
general, almost any biological 1.7.2 Comparison to a Reference
measurement is related to biological
integrity, but some are more clearly As noted earlier, establishing biocriteria
tied to the properties of biotic includes determining the reference
systems of concern to society (e.g., condition. The reference condition
native species, fish production, establishes the basis for making
diverse trophic structure) (Suter comparisons and for detecting use
1993); impairment. Because absolutely pristine
estuarine and coastal marine habitats
< Responsive to Environmental probably do not exist, resource
Stresses Biological measurements managers must decide on acceptable
and the metrics developed from levels of minimum impacts that exist or
them must respond to environmental that are achievable in a given region.
stress. Metrics that are not Acceptable reference conditions will
monotonic; i.e., they do not differ among geographic regions and
consistently exhibit low values in states because estuarine salinity
response to one end of a stressor gradients, trophic state, bottom
continuum and high values in sediment types, morphology and
response to the opposite end, or that biological communities differ between
respond oppositely to different regions.
stresses, are difficult to interpret in
practice; Reference conditions can be established
in a variety of ways. It is important to
< Measurable with Low Error recognize that the reference condition is
Variability and measurement error best developed from a population of
should be controllable so that a sites, not from a single site. However, in
reasonable sampling effort yields some instances, particularly coastal
sufficient precision. Index period environments and sites influenced by
sampling; i.e., sampling during controversial land uses, the use of site-
specific time periods in the annual specific nearfield/farfield stations may
cycle, is one way to reduce seasonal be necessary and appropriate to
variability. However, there are costs augment the reference condition. They
in terms of information derived should include information derived
which may be prohibitive (see later from:
discussion on seasonality);
< Historical Data are usually available
that describe biological conditions in
the estuary or coastal marine region complex and often untestable
over some period of time in the past. hypotheses (Oreskes et al. 1994,
Careful review and evaluation of Peters 1991);
these data provide insight about the
communities that once existed < Expert Opinion/Consensus A
and/or those that may be consensus of qualified experts is
reestablished. Review of the always needed for assessing all of
literature and existing data is an the above information; establishing
important initial phase in the the reference condition; and helping
biocriteria development process. develop the biocriteria. This is
However, if data have not been especially the case in impaired
collected for this specific purpose, locales where no candidate reference
they need to be carefully reviewed sites are acceptable and models are
before being applied; deemed unreliable. In these cases,
expert consensus is a workable
< Reference Sites are minimally alternative used to establish
impaired locations in the same or reference "expectations". Under
similar water bodies and habitat such circumstances, the reference
types at which data are collected for condition may be defined using a
comparison with test sites. consensus of expert opinion based
Reference sites could include sites on sound ecological principles
that are away from point sources or applicable to a region of interest.
concentrated nonpoint loadings; sites The procedures for these
in sub-estuaries; sites occurring determinations and decisions
along impact gradients should be well documented for the
(nearfield/farfield); and regional record.
reference sites that may be applied to
a variety of test sites in a given area; 1.7.3 Assessment Tiers
< Models include mathematical Biological surveys of estuaries and

models (logical constructs following coastal marine waters can be
from first principles and implemented in several tiers, ranging
assumptions), statistical models from a simple and inexpensive screening
(built from observed relationships to detailed field sampling, analysis, and
between variables), or a combination assessment. The tiered approach gives
of the two. Paleobiological agencies one suggested approach for
reconstructions of historic or planning, organizing, and implementing
prehistoric conditions are typically biological surveys. Other approaches
statistical or empirical models may also be available. Agencies should
(Latimer et al. 1997, Alve 1991, Dixit consider the approach that would work
et al. 1992). The degree of best to meet their program objectives.
complexity of mathematical models The tiers are intended to be
to predict reference conditions is implemented cumulatively, that is, each
potentially unlimited with attendant tier should incorporate the elements in
increased costs and loss of predictive the preceding tier as appropriate for the
ability as complexity increases waters in which they are applied. Each
(Peters 1991). Mathematical models integrated tier includes both biological
that predict biological reference and habitat components. Higher tiers
conditions should only be used with require successively more effort and
great caution, because they are yield more detailed information on

specific biotic assemblages and potential as historical data for the area, leads to an
stresses on the system. Higher tiers initial classification of sites and
reflect higher quality information and identification of candidate reference
reduced uncertainty in the final sites.
assessment (Costanza et al. 1992). A
desktop screening and three field survey Tier 2 is somewhat more complex. A
tiers are described in this document. higher level of detail is incorporated into
Figure 1-4 provides a summary of the the standardized biological methods and
requirements for each tier. multiple visits to the site are made to
address temporal variability and/or
Tier 0 is a desktop screening assessment seasonality. Another assemblage
that consists of compiling documented (epibenthos) could be selected in
information for the estuary or coastal addition to those listed above. Water
marine areas of concern through a column nutrient measurements are
literature search and sending survey added to the Tier 1 water column
questionnaires to local experts. No field characteristics. A tactile categorization
observations are made at this assessment of grain size, plus total organic carbon,
level. Desktop screening should precede are added to the bottom characteristics.
any of the three subsequent tiers. Its The data collected in this tier will allow
purpose is to support the planning for the development of preliminary
monitoring and more detailed biological criteria.
assessments. Information to be compiled
in Tier 0 includes: area and Tier 3 is the most rigorous survey tier.
geomorphometric classification, habitat Three or more assemblages are sampled
type, watershed land use, population here, through multiple site visits to
density, NPDES discharges, water account for seasonal variations in the
quality data (salinity, temperature, DO, selected estuarine and coastal marine
pH, turbidity), biological assemblage biological assemblages and should
data, and water column and bottom incorporate supplemental studies which
characteristics. might be necessary for diagnostic
assessment of the potential causes of
Tier 1 is the least complex of the survey observed impairments. This tier adds
approaches. It consists of a one-time water column pesticides and metals
visit to sites during a suitable, measurements, plus full grain size
predetermined index period to collect characterization (sieving to determine
biological and habitat data using percent grain size composition), acid
standardized methods. The focus of this volatile sulfides, and sediment
tier is on developing screening or survey contaminants. This tier also allows the
information. These variables include a resource agency to develop a database
rudimentary identification of organisms sufficient to support resource
(benthos, fish, macrophytes, or management activities to reduce the
phytoplankon), water column identified impairments and to develop
characteristics (salinity, temperature, and refine biocriteria.
DO, pH, Secchi depth, water depth), and
bottom characteristics (grain size, RPD Biological Assessment
layer depth, total volatile solids, and
sediment toxicity). States may choose The procedure of biological assessment
some variation of this list depending on is to sample two or more biological
regional characteristics and resources. assemblages and record data such as
Evaluation of the data collected, as well abundance, condition, biomass, and
Figure 1-4
General
comparison of Tier 0
Tiered -No field observations
Approach.
-Desktop screening
Tiers are
intended to be -Literature search
implemented -Ques tionna ires to local expe rts
cumulatively. -Support planning for monitoring and more detailed
Each tier ass ess m ents
should
incorporate the
elements in
the preceding Tier 1
tier as -One time visit to sites during suitable, predetermined index period
appropriate for -Least complex survey approach
the waters in -Develop screening/survey information
which they are -States choose variation of variables (assemblages + water column &
applied, as
bottom characteristics) according to regional characteristics & resources
necessary for
specific -Leads to initial classification & ID of candidate reference sites
programs.
Tier 2
-2 or m ore visits to site
-More complex
-Possible to add another assemblage
-Add to water column & bottom characteristics samples
-Allows for developm ent of pre lim inary bio logical criteria
Tier 3
-4 or more visits to sites
-Most rigorous
-3 or more assemblages
-Incorporate supplemental studies
-Additions to water column & bottom characteristics
-De velop databas e to supp ort res ourc e m ana gem ent activities to re duc e im pairm ents
& define/refine biocriteria
other characteristics of each species. expected total score under reference

These data are then used to calculate conditions, and the assemblage as a
metrics, such as taxa richness, percent whole is assigned an ordinal rating of
dominance, number of intolerant species, good, fair, or poor. This second
and percent abundance of tolerant comparison to reference conditions is
species. Each metric is compared to its necessary because not all metrics are
expected value under reference expected to score "good" at all times
conditions, and rated good (similar to even in pristine conditions; the final
reference), fair (different from reference), assemblage score thus takes into account
or poor (substantially different from natural variability in metric values.
reference). Numeric scores are assigned
to the ratings, and the scores of all Once these values are satisfactorily
metrics of an assemblage are summed for established they can be incorporated in
a total score for the assemblage. The the development of a biocriterion for a
total score is again compared to the particular estuarine or coastal marine

class. “Biological assessment” at this
point becomes a comparison of
monitoring scores to the biocriteria for
management decision making. The
following several chapters describe the
processes necessary to the development
of suitable metrics and finally their
incorporation in biological criteria for
water resource management decision
making.
Chapter 2
Biological Survey
2.1 Indicators of Biological < The use of indexes to compile and

evaluate large amounts of biological
Integrity data for evaluation.
A key concept underlying the approach
to biological surveys presented in this The suitability of many of the
document is that of biological integrity. approaches in each of these categories
Biological integrity, discussed in greater has long been the subject of debate
detail in Section 1.7, may be among biologists and natural resource
operationally defined as managers. The following discussion
examines both the utility and
“...the condition of the aquatic uncertainty surrounding these
community inhabiting unimpaired community assessment tools.
waterbodies of a specified habitat as
measured by community structure 2.2 Primary Measures of
and function (USEPA 1990).” Community Condition
and Change
Biological integrity is an ideal condition;
estuarine and coastal marine Whenever possible, the investigator
communities can approach a condition should try to examine two or more
of biological integrity when they are assemblages because different organism
minimally impaired by human activities. groups react differently to perturbation.
In order to determine the degree to The more diverse the measures used, the
which these communities approach more robust the investigative technique
biological integrity, it is necessary to is and the more confidence the manager
measure attributes (or indicators) of can place in the results. However, this
community structure and function and idea must be reconciled with the
to be able to distinguish between natural limitations of the costs of multiple and
variations and anthropogenic impacts. diverse surveys and the relative
availability of reliable scientific methods
Various techniques can be used at any to measure some assemblages. The
level to document the effects of prevalent approaches today are
anthropogenic perturbations on measures of benthic macroinvertebrate
biological communities. Discussion of infauna, fish, and aquatic vegetation.
these techniques falls into three general
areas, the first two of which are 2.2.1 Benthic Macroinvertebrates
measurement processes and the third is
a data processing technique. They are: The benthic infauna have long been
used for water quality assessments
< Measures of community condition because of their tendency to be more
and change; sedentary and thus more reliable site
indicators over time compared to fish
< The presence or absence of indicator and plankton. Consequently, a larger
taxa; body of data has been accumulated for
this assemblage. Examination of benthic
community structure and function is a < Current methods can distinguish
valuable tool for evaluating the severely impaired sites from those
condition of benthic habitats, for that are minimally impaired.
monitoring rates of recovery after However, it can be difficult to
environmental perturbations and discriminate between slightly or
potentially to provide an early warning moderately impaired areas,
of developing impacts to the system. particularly in estuaries (due to their
Bilyard (1987) and USEPA (1991) cite the natural spatial and temporal
following specific advantages of variability);
monitoring benthic infauna to determine
overall aquatic community health: < The condition of benthic habitats can
vary over relatively small scales.
< Benthic infauna are typically Therefore, if too few samples are
sedentary and therefore are most collected from a specified area, the
likely to respond to local ambient heterogeneity to be
environmental impacts, thus expected may be missed, potentially
narrowing the list of possible causes leading to incorrect conclusions
of impairment; regarding the biological and water
quality conditions in the area;
< Benthic infauna are sensitive to
disturbances of habitat such that the < The cost and effort to sort, count,
communities respond fairly quickly and identify benthic invertebrate
with changes in species composition samples can be significant, requiring
and abundance; tradeoffs between expenses and the
desired level of confidence in
< Benthic infauna are important decisions based upon the collected
components of the food chain and data.
often act to transport not only
nutrients, but also toxicants, to the 2.2.2 Fish
rest of the system;
Fish are an important component of
< Monitoring benthic infauna provides estuarine and marine communities
an in situ measure of relative biotic because of their economic, recreational,
integrity and habitat quality; aesthetic and ecological roles. The
abundance and health of the fish
< Of the biota typically measured, this community is also the primary indicator
assemblage has the strongest used by the public to discern the health
supporting database. Thus, it has of a water body. Fish are good
extensive historical and geographic indicators of ecological health because:
application.
< They are relatively sensitive to most
Some limitations of benthic infauna habitat disturbances;
sampling include:
< Being mobile, sensitive fish species
< Relatively few state and federal may avoid stressful environments,
programs have the necessary in- leading to measurable population
house taxonomic expertise to patterns reflecting that stress;
support extensive monitoring
activities;
2-2 Biological Survey

< Fish are important in the linkage < Fish surveys may be biased because
between benthic and pelagic food of recreational and commercial
webs; fishing pressures on the same or
related fish assemblages;
< They are long-lived and are
therefore good indicators of long- < Some fish are very habitat selective
term effects; and their habitats may not be easily
sampled (e.g., reef- or marsh-
< They may exhibit physiological, dwelling species);
morphological, or behavioral
responses to stresses; < Since they are mobile, spatial
variability is very high, requiring a
< Fish may exhibit obvious external large sampling effort to adequately
anatomical pathology due to characterize the fish assemblage.
chemical pollutants;
2.2.3 Aquatic Macrophytes
< Fish databases originally compiled
to support state and federal fisheries Aquatic macrophytes in estuarine and
management programs may be coastal marine waters may include
available. These databases may vascular plants (e.g., seagrasses) and
require integration with other data algae (e.g., sessile and drift). Vascular
(e.g., water quality) to be useful for aquatic macrophytes are a vital resource
bioassessment and biocriteria because of their value as extensive
purposes. primary producers in estuaries. They
are a food source for waterfowl, a
The limitations on the use of fish in habitat and nursery area for
community bioassessments include: commercially and recreationally
important fish species, a protection
< Fish represent a relatively high against shoreline erosion, and a
trophic level, and lower level buffering mechanism for excessive
organisms may provide an earlier nutrient loadings. The primary
indication of water quality problems; productivity that has been observed for
submerged aquatic vegetation (SAV)
< Some fish are resident species with communities in estuaries is among the
relatively limited lifetime spatial highest for any aquatic system (USEPA
ranges. Others have relatively large 1992). Excessive nutrient loadings lead
ranges, making it difficult to isolate to prolific phytoplankton and epiphytic
probable causes of degradation that macroalgal growth on seagrass which
could occur anywhere within their out-compete the seagrass through
range. Thus, the spatial scale of shading, as evidenced by the 1970s and
sampling is an issue and because of 1980s decline of eelgrass in the
seasonal, open water migrations, Chesapeake Bay along with the current
temporal adjustments may also be decline in Waquoit Bay. Because of the
necessary; combined high productivity and habitat
function of this plant community, any or
< Mobile organisms such as fish may all of the other estuarine or coastal
avoid stressful environments, marine biota can be affected by the
reducing their exposure to toxic or presence or absence of macrophytes.
other harmful conditions;
Some of the advantages of using aquatic necessarily related to changes in
macrophytes in biological surveys are: water quality;
< Vascular plants are a sessile < Aquatic macrophytes do not stand
community. There is essentially no alone as an indicator of ecosystem
mobility to rooted vascular or condition; additional parameters
holdfast-established algal plant (e.g., water column nutrient
communities, so expansion or concentrations, light penetration) are
contraction of seagrass beds can be required to interpret macrophyte
readily measured as an data.
environmental indicator;
2.2.4 Phytoplankton
< Measurement of macrophyte
community extent and relative Many estuaries and marine waters can
density can be fairly easily be considered "plankton-dominated"
accomplished by remote means, systems, which implies that this
such as aerial photography, if the assemblage should provide valuable
water is clear or shallow; information in an assessment of
ecosystem condition. Advantages of
< Sampling frequency is reduced using plankton include:
because of the relatively low
community turnover compared to < Plankton provide the most notable
other biota such as benthic indication of eutrophication in
invertebrates or fish; estuarine environments. Changes in
nutrient concentrations can result in
< Taxonomic identification in a given long-term changes in estuarine
area is generally consistent and community structure and function
straight-forward. and planktonic primary producers
are one of the earliest communities
Some of the disadvantages of to respond;
macrophyte surveys are:
< Changes in plankton primary
< Relatively slow response by the production will in turn affect higher
plant community to perturbation trophic levels of macroinvertebrates
makes this a delayed indicator of and fish;
water quality impacts. This could be
critical if prompt management < Many states routinely monitor
responses are needed; chlorophyll a as part of water quality
monitoring due to the ease and
< Successional blooms of some relatively low cost of analysis;
macrophytes means seasonal cycles
need to be identified and < Plankton have generally short life
accommodated by the survey cycles and rapid reproduction rates
schedule to avoid misinterpretation making them valuable indicators of
of data and false assumptions of short-term impact.
water quality impacts;
As with all other assemblages, there are
< Changes in abundance and extent of disadvantages associated with using
submerged macrophytes are not phytoplankton in a biosurvey:

< The fact that phytoplankton are be incorporated in biocriteria
subject to rapid distribution with the development and environmental
winds, tides, and currents means management decision making.
they may not remain in place long Paleoenvironmental reconstruction is an
enough to be source identifiers of additional technique being developed.
short-term impacts. This problem is This technique allows investigators to
compounded by the ability of some infer past conditions from the remains of
phytoplankton to synthesize several groups of organisms found in
atmospheric sources of nitrogen, sediment cores, and to compare those
thus confounding the identification past conditions to current ones.
of runoff sources of nutrients in
estuaries and the resultant changes 2.3.1 Zooplankton
in the aquatic biota;
Zooplankton consist of two basic
< Taxonomic identification of categories: holoplankton which spend
phytoplankton can be difficult and their entire life cycle as plankton, and
time-consuming; meroplankton which are only plankton
while in the larval life stage.
< Competition by aquatic
macrophytes, higher respiration Holoplankton are characterized by rapid
rates, and increased grazing by growth rates, broad physiological
zooplankton may counteract tolerance ranges, and behavioral
increased phytoplankton biomass patterns which promote their survival in
resulting from nutrient enrichment. estuarine and marine waters. The
These reasons argue for calanoid copepods are the numerically
investigating phytoplankton and dominant group of the holoplankton,
zooplankton together as biological and the genus Acartia (A. tonsa and A.
indicators; clausi) is the most abundant and
widespread in estuaries. Acartia is able
< Phytoplankton can undergo blooms, to withstand fresh to hypersaline waters
the causes of which might be and temperatures ranging from 0o to
indeterminate, at varying 40oC.
frequencies.
The meroplankton are much more
2.3 Measures of Community diverse than the holoplankton and
consist of the larvae of polychaetes,
Condition and Change
barnacles, mollusks, bryozoans,
Being Developed echinoderms, and tunicates as well as
the eggs, larvae, and young of
Two assemblages (zooplankton,
crustaceans and fish.
epibenthos) have considerable potential
for expanding the biological information
Zooplankton populations are subject to
available for biocriteria development
extensive seasonal fluctuations reflecting
and bioassessments. These assemblages,
hydrologic processes, recruitment, food
however, are considered
sources, temperature, and predation.
“developmental” at this time. As survey
They are of considerable importance as
methods become more refined and
the link between planktonic primary
routine, databases for these assemblages
producers and higher carnivores. As
will expand and the techniques are
such, they are also early indicators of
expected to become sufficiently robust to
trophic shifts in the aquatic system.
Advantages of zooplankton sampling composition reflects the average
are similar to phytoplankton: salinity, temperature and dissolved
oxygen of that locale over an
< The rapid turnover of the extended period of time (Day et al.
community provides a quick 1989);
response indicator to water quality
perturbation; < Ease of data collection by use of
small otter trawls or beam trawls;
< Sampling equipment is inexpensive
and easily used; < Relative ease of identification
because taxonomic lists of local
< Compared to phytoplankton, sorting crustaceans, mollusks, and
and identification is fairly easy. echinoderms can be fairly easily
compiled;
Some limitations of using zooplankton
in biosurveys are: < Sampling is as inexpensive as fish
surveys, and can often be done with
< The lack of a substantial data base the same or similar equipment
for most regions; during the same survey;
< The high mobility and turnover rate < Decapod crustacea are usually very
of zooplankton in the water column. important prey for fish and are
While this permits a quick response important components in benthic
by zooplankton to environmental food webs. Some (e.g., shrimp and
changes on the one hand, it also crabs) are harvested for human
increases the difficulty of evaluating consumption.
cause and effect relationships for this
assemblage. Possible difficulties involve:
2.3.2 Epibenthos < Potential equipment snags and

difficulties in macrophyte beds;
The sampling of those animals living on
the sediments or on structures may < Benthic infauna would likely be
prove to be the link between relatively included in the trawl sample due to
low cost but highly variable fish disturbance of surface sediments;
community information, and the more
consistent but expensive benthic < As when using otter trawls for fish,
macroinvertebrate surveys. The process benthic habitat may be destroyed;
has been tested with considerable
success in Washington, North Carolina, < There is greater potential for
and Florida (Chapter 13). avoidance by organisms than when
sampling for benthic
Advantages of using this assemblage macroinvertebrates, though not as
are: great as with fish surveys;
< The relatively sedentary life style of < Because of relatively low taxa
some epibenthic fauna can result in numbers in some environments,
an in-place accumulation of especially coastal marine waters,
indicative pathogens and toxicants impact response may not be as
in individuals while the community sensitive as desired; this could be

addressed by the use of indicator < paleoenvironmental reconstruction
species instead of a multimetric can provide a site-specific reference
approach; by showing conditions in the past.
< Epibenthos are very sensitive to Disadvantages of studying

substrate type; paleoenvironmental systems include:
< Relative sensitivity remains to be < it requires a relatively stable

determined in many areas. depositional environment; it is not
suitable for shallow estuaries subject
2.3.3 Paleoenvironmental to frequent resuspension;
Reconstruction: preserved
remains < it requires conditions for
preservation of target assemblages in
Several groups of organisms in estuaries the sediment;
leave remains in the bottom sediments.
Some of the remains are resistant to < temporal resolution is limited by the
decay and become a permanent rate of accumulation (between 1-10
biological record of the life in that years); it cannot be used to assess
waterbody. Comparisons of present-day short-term response to stressors or to
biota to that of the past allow past restoration efforts;
environmental conditions to be inferred.
Several groups of organisms have been < at the time of this writing, technical
used for this type of study in estuaries expertise for estuarine paleoecology
including diatoms, dinoflagellates, and is specialized, with only a small
foraminifera (Latimer et al. 1997). handful of research institutions
active in North America.
The approach is to elucidate
relationships between environmental 2.4 The Use of Indexes to
conditions (for example, temperature, Compile And Evaluate
dissolved oxygen, nutrient
Biological Data
concentrations) and the relative
abundance of target species. These
It is evident that biological surveys can
known relationships are then used to
generate tremendous amounts of raw
infer past conditions from the observed
data. The usual approach to sorting this
remains in the sediment. Advantages of
wealth of observations is to summarize a
studying paleoenvironmental systems
series of diverse community
include:
measurements into one or more
dimensionless indexes, much as the
< diatoms, dinoflagellate cysts, and
cumulative performance of a student's
foraminifera found in sediments
work for a year can be reduced to
integrate conditions over broad
annual grades.
spatial scales and over time periods
of one year or more, so that short-
As with student grades, the use of
term variability does not confound
dimensionless indexes is a well-
assessment;
established and consistent way to
evaluate and compare many discrete
< there is no need to adhere to an
units as a continuum of performance or
index period for sampling;
condition. Also similar to student
grading, detailed insight is lost when the < Provides no indications of causes of
complex interplay of so many discrete the relative condition of the system.
variables is reduced to a single score.
The reasons for high or low scores are The best way to guard against the
not always evident and the accuracy of problems of indexing, while using it to
the scoring process itself is always expedite decision-making, is to always
subject to debate. Indexing is the only retain the raw data. These files can be
way to rank order information for used to translate historical data sets into
decision making. However, valuable present indexes for temporal continuity,
insight is lost at every level of data and even more important, they can be
reduction. There is no alternative to the evaluated to provide an interpretation
process short of relying entirely on the and potential diagnosis for management
professional judgment and wide action when a particular site is being
variation of skill of individual biologists. evaluated.
The strengths of index development and
use are: Indexes are most often used to measure
community composition such as species
< It is a rational, consistent way to abundance, diversity, evenness,
reduce large amounts of data to richness, and dominance or conditions
unitless, meaningful interpretations; such as incidence of disease,
malformation, and distributions of year
< It is a quantitative treatment of the classes. These can be used to assess the
observations which permits changes in community structure that
statistical assessments; occur as a result of anthropogenic
perturbations (Boyle et al. 1990).
< Interpretive bias is reduced in the Community function can also be
treatment of the data. described through indexes such as the
Infaunal Trophic Index (Word 1978,
Conversely, indexing: 1980, USEPA 1987).
< Removes the decision-making from Although indexes have long been used
detailed evaluation of the data and in applied and theoretical ecology, it is
information to just reporting of recognized that some of them, when
simplified indexes; applied individually, are insensitive to
stress-induced changes in naturally
< May be viewed as irrefutable, occurring biological communities (Boyle
despite evidence to the contrary; et al. 1990). Because of varying
sensitivities of the community indexes,
< May obscure important and several of them should be used
confounding interrelationships in concurrently for evaluating impacts.
the aquatic environment This approach provides greater certainty
contributing to the index score(s); of the data interpretation than reliance
< Obscures more information as each on any single index. Conversely, while
level of data reduction is performed Ludwig and Reynolds (1988) indicate
leading to an index value, so that that the most reliable community
some indexes are not sufficiently measures in evenly matched surveys are
sensitive to reflect biotic change; number of individuals and number of
taxa as direct measures; it has been

observed in the coastal marine studies toxic to R. abronius (Swartz et al. 1985).
associated with this guidance manual More studies performed by Swartz et al.
that, at least in two mid-Atlantic Bight (1994) at a designated Superfund site in
outfall studies, the diversity index and San Francisco Bay also showed that
the richness index both appear to be acute sediment toxicity lab tests of R.
more responsive than number of abronius correlated with biologically
individuals or number of taxa to sewage adverse sediment contamination in the
impacts (Gibson, Chapter 13). For a field. Other EMAP studies (Summers et
more detailed discussion of the different al. 1992) included a 10-day acute test
indexes and their particular applications using the tube-dwelling amphipod,
see Chapter 11 (Index Development) Ampelisca abdita. The majority of
and Chapter 13 (Case Studies). sediments proving significantly toxic to
A. abdita were found in Louisiana and
2.5 Indicator Taxa Alabama estuarine waters.
Indicator taxa or species are those A well-known indicator for degraded

organisms whose presence (or absence) systems is the polychaete Capitella
at a site indicates specific environmental capitata. C. capitata and its related
conditions. If an organism known to be species are collectively known as the C.
intolerant of pollution is found to be capitata complex. In general, the
abundant at a site, high water quality presence of this indicator species
conditions can be inferred. On the other corresponds to a dominance of deposit
hand, dominance by pollution tolerant feeders that colonize an area as organic
organisms implies a degraded condition. pollution increases. Swartz et al. (1985)
When available, indicator taxa are an observed dominance of Capitella near
important, cost-effective preliminary sewage outfalls. A recent study in the
survey tool for site assessments. Mid-Atlantic Bight by the U.S. Army
However, the investigator should Corps of Engineers (1996) suggests that
always ascertain that absence of an the polychaete Amastigos caperatus may
indicator organism is a fact and not have indicator potential similar to the
merely a reflection of insufficient Capitella complex.
sampling.
A problem with using pollution tolerant
Swartz et al. (1985, 1986, 1994) have indicator organisms is that some of these
demonstrated the sensitivity of the organisms may be ubiquitous and found
amphipod Rhepoxynius abronius to the in naturally occurring organically
complex contaminant mixture that often enriched habitats as well as in minimally
characterizes coastal marine benthic impaired waters. To be useful as an
pollution. Their studies were performed indicator, they must have displaced
along pollution gradients from the Los other, less robust taxa and have
Angeles County Sanitation Districts’ achieved numeric dominance. Tolerant
sewage outfalls to control conditions in and ubiquitous organisms can be found
Santa Monica Bay. The results showed in sediments far away from sources of
that there were significant increases in sewage pollution and long after plumes
the concentration of most sediment have dispersed.
contaminants and significant decreases
in benthic taxa richness and abundance The use of the concept of "clean"
at stations where sediment was acutely indicator species is less subject to this
form of misinterpretation. These "clean"
or highly sensitive organisms are less including pollution sensitive ones and
likely to be found in both polluted and some that are pollution tolerant.
high quality habitats.
The best option may be the paired use of

both pollution tolerant and intolerant
indicator species. If both indicators
change concurrently in opposite
directions, more confidence can be
placed in the interpretation.
As part of the biological survey process,

individual indicator species are useful in
reducing analytical costs. They are not
only a valuable preliminary assessment
tool, they are a cost-effective way to
define the magnitude, spatial, and
temporal extent of an impact (USEPA
1992). Selected indicators should
possess the following characteristics
(Green 1984):
< Provide sufficiently precise and

accurate appraisals of:
— species of concern
— magnitude of anthropogenic
disturbance;
< Be cost-effective and statistically

reliable as an alternative to
monitoring all critical community
measures;
< Appropriate to the spatial and

temporal scale demanded by the
study objectives.
When indicator species are employed in

tandem for impact investigations, a
gradient of species distribution can often
be identified. Such a gradient might
progress from the most degraded
waters, having low diversity
communities dominated by pollution
tolerant opportunistic species, to
unimpaired or minimally impaired
waters having diverse communities that
are comprised of a wide range of taxa,

Chapter 3
Habitat Characterization
Biological assessment in estuaries and habitat including discharges,

coastal marine waters is built around agriculture, and urban land use which
assessing two separate ecosystem contribute materials (sediment,
nutrients, contaminants) to the water
components: the habitat and the biota.
body. Biological communities are
The biota are the resident plant and directly affected by their physical
animal assemblages in the water body. habitat and water quality conditions,
The condition of the biota depends in and also by direct human activities such
part on the quality of the physical- as stocking or harvesting.
chemical environment of estuaries and
coastal marine waters; i.e., habitat. Components of biota are the biological
Habitat is in turn influenced by natural assemblages, such as algae, aquatic
and catastrophic events, climate, and macrophytes, benthos, epibenthos,
human activities. These include: plankton, and fish. Habitat components
for the biological assessment of these
Seasonal variations in precipitation, assemblages are hierarchical, and
temperature shifts, and wind or include the watershed, the nearshore
wave patterns; zone, the water column, and the
sediment. An integrated assessment
Introduced or extirpated species able evaluates the condition of estuaries and
to influence the habitat (such as coastal marine waters by aggregating
burrowing organisms, plants, or data on components of both habitat and
diseases/parasites; biota. The habitat component may be
damaged by physical stress or chemical
Shifts in sedimentation or scouring degradation from pollution. Thus,
patterns; habitat studies may help identify causes
of biological decline as well as being the
Dredging and filling; important determinant of the types of
biotic communities to be expected. This
Shoreline or basin construction; classification function is crucial to
proper biocriteria development.
Bulkheading and jetty construction;
Habitat characterization is essential to
A variety of land use and the proper classification of sites.
navigational practices. Although estuaries are by definition
transitional zones between fresh water
This conceptual model is based on an and the sea, and both estuaries and
understanding of the causal mechanisms coastal marine waters incorporate many
of natural and anthropogenic stress environmental gradients (e.g., salinity,
effects in estuarine and coastal marine sediment grain size, depth), individual
ecosystems. locations and conditions are often
defined categorically. Thus, a site may
Estuaries integrate processes because
be characterized as oligohaline or
they receive and retain matter and
energy released in the watershed. Many mesohaline with respect to salinity, or
human activities directly affect aquatic sand or mud with respect to sediment
grain size. The composition of Depth—stronger interactions
biological assemblages can vary between the water column and the
dramatically along these habitat bottom occur in shallow estuaries,
gradients, and valid comparisons of thereby expediting the release of
estuarine and coastal marine biological sediment nutrients for use by the
assemblages require that their habitats phytoplankton;
be correctly classified.
Variability of salinity and the
3.1 Flow and Hydrography sharpness and pattern of the salinity
gradient from the mouth to the
The type of estuarine ecosystem in a headwaters. Water circulation
specific area is primarily controlled by influences the salinity gradient and
the physical environment; i.e., the distribution of biological
geomorphology, climate, salinity, and assemblages;
the availability of fresh water. The
absolute values of the abiotic factors are The rate of geomorphological change
not as important as the degree of generated by various physical forces
fluctuation of factors such as the that control sediment transport
microclimate, water movement, within the estuary.
chemical cycling, and physical structure
(Day et al. 1989). In addition, the These controlling abiotic features are
residence time of water in an estuary can discussed in more detail in the following
influence overall water column sections.
pollutant concentrations.
3.1.1 Circulation and Tidal Regime
The abiotic features thought to be
important in determining the specific Circulation is the physical process that
nature of estuaries as proposed by Day influences or controls many of the
et al. (1989) are: ecological processes occurring in an
estuary, including the degree to which
The degree of protection and an estuary is dominated or modified by
buffering from direct oceanic forces; hydrodynamics. The three major
driving forces behind the circulation
The quantity of freshwater input and patterns in estuaries are: (1)
associated dissolved and suspended gravitational circulation; (2) tidal
materials; circulation; and (3) wind-driven
circulation. Geostrophic forcing; i.e., the
The water circulation patterns that Coriolis effect, can significantly alter
are determined by riverine and tidal estuarine circulation patterns as does
currents, geomorphology and wind. bathymetry. A notable example is the
Tides play a critical role in Chesapeake Bay, where lower salinities
influencing circulation, and extend further south along the Bay’s
biochemical and biological western shore in comparison to its
processes. In many coastal regimes, eastern shore.
the wind-driven currents are more
predominant than tidal and Gravitational circulation is induced by
geomorphologically-induced water masses of differing densities and
currents; the layering of fresh water inflow on top
of more saline waters. These density
differences cause the lighter fresh water
3-2 Habitat Characterization

to flow over top of the saltwater to form or wind stress. In many estuarine
what is commonly termed the "salt systems, gravitational and tidal effects
wedge". In what is termed the coexist.
"classical" estuarine gravitational
circulation, the pressure surfaces of the Wind circulation is common in estuaries
fresh water are tilted seaward and the with open water, shallow water depths,
pressure surfaces of the saltwater are a small tidal range, and low fresh water
tilted toward the head of the estuary. input. Although the effects of wind may
The shear stress forces that occur at the be overshadowed by gravitational or
interface of these two water masses tidal forces, periods of sustained wind
cause vertical mixing and an eventual can have dramatic ecological effects. In
equalizing of the pressure surfaces the Ten Thousand Islands region of the
somewhere near mid-depth. The fresh Florida Everglades, sustained northern
water surface layer has a net seaward winds virtually drain the water out of
movement, the saltwater layer on the large portions of the estuary for
bottom has a net movement upward into extended periods of time, exposing large
the estuary and the interface is a zone of areas of mudflats. Winds that blow into
no net movement. an estuary can create a net flood flow
and result in the inundation of marshes
Typically, density differences and the and grass lands. In lagoons as well,
resulting circulation are determined by water can pile up on one side of the
salinity and the circulation as is lagoon creating a seiche or a sloshing of
described above. However, in arctic or the water back and forth within the
subarctic estuaries, the fresh water lagoon.
inflow may be substantially colder than
the saltwater causing the fresh water Attention to these diverse, often
inflow to sink below the saltwater, variable, and always significant
reversing the expected circulation circulation patterns is essential to
pattern. In shallow lagoons that receive understanding the biotic distribution of
little or no fresh water input such as coastal and estuarine environments.
Florida Bay or Laguna Madre, the This must always be addressed before
evaporation rate can cause the salinity of attempting to attribute such distribution
the water within the lagoon to rise to anthropogenic influences.
higher than the ocean waters. When this
happens, the ocean water flows into the 3.2 Habitat Types
estuary on the surface and the estuarine
water flows out on the bottom, resulting Use of a single habitat to characterize
in reverse circulation. Most often, biological assemblage condition would
though, shallow lagoons are well-mixed minimize the requirements for
by the wind and reverse circulation is expenditure of time and resources.
only observed at the mouth of the However, estuaries and coastal marine
lagoon. waters are inherently heterogeneous
systems. By definition, a salinity
Tidal circulation occurs when the ebb gradient is present in any estuary.
and flow of the tides becomes the Greater numbers of species are typically
driving force behind circulation. This is observed at the marine end of the
known to occur in estuaries with steep salinity gradient, with the fewest
constrictions or with shallow depths and numbers observed in about 3-7-ppt
large tidal ranges (e.g., Puget Sound),
(Weisberg et al. 1993). This may be due
and in the absence of density gradients
to the unpredictable nature with which
the brackish water zone varies along the should be noted that not all
length of the estuary; driven by the phytoplankton blooms (e.g., red tides)
strength and intervals of freshwater result from anthropogenic stresses.
inflow. Increases in the standing stocks of
bacteria associated with fecal material
In addition to a salinity gradient, can be used to identify the presence of
estuarine habitats vary in bottom sewage effluent. Open water (plankton
substrates, and in the predominance of and nekton) studies also allow
erosional versus depositional assessment of pelagic food webs.
environments. The variations in these Sampling of pelagic finfish also occurs
characteristics will lead to differences in in open estuarine and marine waters.
the way pollutants and other stressors Limitations of sampling in open water
will effect the biota. For example, include a high degree of patchiness in
depositional environments occur where the plankton and finfish assemblages,
large amounts of terrigenous sediments which necessitates the sampling of large
are transported by rivers to embayments volumes and areas of water before
and where the water is sufficiently results can be described with acceptable
quiescent that fine-grained sediments precision. Because of the transitory
settle out. Metals, synthetic organic residence time of water parcels moving
pollutants, and other contaminants through estuaries and the short life
adsorb to fine-grained sediments cycles of planktonic flora and fauna, a
(Holland 1990) and low-density organic relatively high sampling frequency is
detritus. Thus, the prevalence of necessary to distinguish signals from
depositional areas may reduce the noise in this area.
likelihood of water column exposure of
estuarine organisms to toxic materials, 3.2.2 Soft Bottom Substrates
but may increase the exposure to
burrowing organisms. Conversely, the A "soft bottom" deposit may be
water column of erosional zones is often dominated by mud or fine- to relatively
highly enriched as resuspended coarse-grained, hard-packed sand. All
phosphorus is episodically mobilized. of these sediments can be sampled with
appropriate grabs. Soft bottom
Habitats in estuaries and coastal marine substrates provide habitat for
waters can be classified into nine major economically valuable clams, shrimp,
categories. These habitats are and juvenile flatfishes. Muds have a
summarized below in a progression high surface area-to-volume ratio,
from open, deep waters to decreasing providing a large surface area for the
depths near the shoreline. The choice to adsorption of metals and organic
sample one or more of these nine pollutants. Also, fine-grained deposits
habitats will be dictated by their areal are often rich in biogenic adhesives
extent and the nature of the problems (mucopolysaccharide secreted by
being addressed. microbes and meio- and macrofauna), to
which organic pollutants may adhere.
3.2.1 Open Water Under anoxic conditions, these deposits
are often called “black ma yonnaise.”
Sampling in open water may Conversely, sands have a lower surface
demonstrate phytoplankton blooms area-to-volume ratio. Thus, there is less
which might be symptomatic of surface area available in the deposit to
eutrophication from anthropogenic which pollutants may adsorb.
inputs of phosphorus or nitrogen. It

A limitation of sampling in soft sampler cannot be used, for example, as
substrates is that the samples must be it can in soft-bottom habitats. Typically,
sieved before individuals can be counted divers conduct transect observations
and identified. With medium or coarse and take photos.
sands this also means large volumes of
sediment are retained on the sieves for Another limitation of sampling hard
subsequent processing. Thus, substrate is that the larvae and spores of
measurements cannot be readily made rocky substrate organisms are typically
in the field. This is especially true for planktonic; therefore, recruitment may
samples in which an abundance of be strongly influenced by factors outside
organic debris (wood chips, seagrass the estuary. Sampling and analysis
leaves) masks the presence of small, methods must be appropriate both to the
cryptic organisms. specific type of hard substrate as well as
regional characteristics due to the fact
3.2.3 Hard Bottom Substrates that hard bottom substrates can exist
from rocky, high energy regions in
Hard bottom substrates can include California to carbonate sediment, low
offshore rocky outcrops; oyster, relic energy regions in Florida.
shell, and worm tube reefs; and relic
limestone and coral outcrops. Oyster 3.2.4 Aquatic Macrophytes
and mussel beds are major habitats
supporting a complex community of Macrophyte beds are among the most
various species essential to the biological important estuarine habitats, both
diversity of estuaries such as ecologically and economically.
Chesapeake, Florida, and Tampa Bays. Seagrasses (in this text, used to describe
In fjords the predominant subtidal macrophytes existing from tidal fresh to
habitat may be the rocky walls marine conditions) create an
extending below the water line. An environment with a high degree of
advantage of sampling these areas is structural complexity. Ecological niches
that the macroalgae growing along these exist within the sediment, between the
walls may be relatively sensitive to rhizomes, along the surfaces of the
stress and can be used in bioassays or leaves, and in the protected portion of
tested for bioaccumulation (Levin and the water column within the bed. Thus,
Kimball 1984). a seagrass bed is capable of supporting a
highly diverse fauna. Seagrass beds are
Hard bottom substrates frequently occur among the most productive aquatic
in high-energy environments common habitats. In western Florida, Thalassia
in portions of Alaska, Washington, testudinum beds produce 8,100-gm-2 dry
Oregon, and northern California, as well weight of leaves at maximum standing
as New England. For example, crop (Hillman et al. 1989). Seagrass beds
gravel/cobble beaches are typically provide "nursery areas" for juvenile
subject to high incident wave energy. fishes and decapod crustaceans,
Accumulations of fine-grained including many of economic
sediments or organic detritus are not importance. Seagrass leaves are known
expected on hard substrates either to bioaccumulate and possibly to
because there is no riverine source or bioconcentrate metals (Ward 1989).
because the energy of the environment
prevents their accumulation. In The right mix of nutrients and water
addition, subtidal rocky bottoms are clarity are key in seagrass growth and
difficult to sample remotely. A grab survival in estuarine systems. A study
by Stevenson et al. (1993) demonstrated energy. These beaches may be
regrowth of SAV in the Choptank River commonly found on the Atlantic coast
of the Chesapeake Bay (mesohaline north of Cape Cod and along the Pacific
salinity regime) was associated with coast. High energy beaches of
mean DIN <10-:M, mean DIP <0.35-:M; southeastern Florida are composed of
mean SPM (suspended particulate sand and are protected by sabellariid
matter) <20-mgL-1 ; mean chlorophyll a reefs offshore. Low energy beaches
(in water column) <15-:gL-1 ; and mean consist of sand and finer sediments and
light attenuation coefficient (Kd)<2-m-1 . are widely located on the Atlantic coast
south of Cape Cod, the Gulf of Mexico,
In addition to serving as habitat for and along the southern Pacific coast,
invertebrates and fish, macrophytes are and along the shorelines of most
also a biological assemblage in their own estuaries and their tidal tributaries.
right and appear to be relatively
sensitive to stress. These beds can be Distinct zones occur across the beach
monitored from historical photos and profile, proceeding from the subtidal
other records (Shepard et al. 1989). offshore and inshore zones, through the
Areal reductions are often attributed to foreshore that lies between the upper
shading, which may result from a current of wave swash at high tide and
variety of anthropogenic factors the low water mark of the backrush of
including turbidity (from ship traffic, the wave swash at low tide, to the
dredging, or harbor construction which subaerial backshore (Komar 1976).
may stir fine-grained material up into These zones contain a gradation of
the water column) and eutrophication faunal communities in response to
(where inputs of nutrients stimulate varying conditions of wave energy,
increases in the density of sediment size, and inundation by water.
phytoplankton and of epiphytic macro- Sampling across the beach profile can be
and microscopic algae on leaf surfaces). problematic, particularly on high energy
beaches, due to the rapidly-varying
A limitation of sampling in seagrass wave conditions and distribution
habitats is that because of their patterns of beach infauna and epifauna.
ecological complexity, multiple If attempted, core samplers can be used
sampling strategies are required to on low energy beaches but quadrat
survey the various components of the surface sampling may be required on
fauna (Howard et al. 1989), increasing high energy beaches.
the expenditure of time and resources by
investigating agencies. 3.2.6 Sandflats
3.2.5 Beaches Deposits described as "fine sand"

contain some silts and clays and harbor
Beaches are accumulations of rich communities of both deposit- and
unconsolidated sediment (e.g., sand, suspension-feeding invertebrates.
cobble) extending shoreward from the "Coarse sands," found in higher energy
near low-tide line to some demarcation environments, are expected to be
such as a sea cliff or dune field, or to the dominated by suspension-feeding
point where permanent vegetation is invertebrates. If a sufficient erosional
established (Komar 1976). High energy force is applied to a sandy bed by the
beaches typically consist of shingle or overlying flow, sand waves form. Sand
cobble due to the removal of finer waves indicate a physically stressful
sediments by high incident wave habitat, typified by a relatively

depauperate fauna. It should be noted fish and wildlife populations. Although
that coarse sands generally contain "microelements" of the marsh
relatively low faunal densities and community (e.g., terrestrial insect
biomass. However, when coarse sands assemblages) may be more sensitive to
are colonized by surf clams and perturbations, these studies may be
echinoderms (sand dollars), densities more expensive and time-consuming to
and biomass can be very high. carry out. For example, insect
Compared to mudflats, relatively little populations are difficult to sample
organic material and few associated quantitatively because of their mobility
pollutants are expected to accumulate in and cyclic abundance.
coarse sands. Calcareous deposits in
Puerto Rico and Hawaii may provide an 3.2.9 Mangrove Forests
exception to this in that they have high
organic matter content and many Low-lying tropical coasts are often
pollutants (Dossis and Warren 1981). bordered by dense mangrove forests.
Temperature, particularly the frequency
3.2.7 Mudflats of freezes, and rainfall gradients restrict
mangrove distribution. In the Gulf of
Mudflats provide habitat for Mexico, mangrove forests occur along
commercially important clams and other the coasts south of Cedar Keys, Florida
invertebrates and feeding habitat for and generally south of Port Isabel,
fishes and shorebirds. Fine-grained Texas. Isolated stands of black
sediments (i.e., clay) and organic mangrove (Avicennia germinans) occur in
detritus accumulate on mudflats. These the Mississippi deltaic plain (Day et al.
materials provide a large surface-to- 1989), but mangroves are otherwise
volume ratio adsorb metals and organic absent from the northern Gulf coast,
pollutants. This same expanse of which is dominated by salt marshes.
usually nutrient and oxygen rich habitat Significant mangrove stands also occur
also supports diverse primary south of Cape Canaveral on the east
producers, bacteria, plankton, and fish coast of Florida (Odum and McIvor
and invertebrate species in a complex 1990). Mangrove forests and their
community. associated waters provide valuable
habitat for a range of invertebrates,
3.2.8 Emergent Marshes fishes, amphibians, reptiles, birds, and
mammals. Mangroves are also valuable
Where present, emergent marshes may as stabilizers of intertidal sediments, and
be extremely important components of the structural complexity of the prop-
estuaries and coastal marine roots provides habitat for many
embayments and lagoons because they commercially and recreationally
filter storm water runoff from cities, important fishes.
forests, and agricultural areas.
Emergent marshes may also provide 3.3 Water Column
flood protection by attenuating peaks in Characteristics
storm water flow and reducing the
erosive energy of wave action. Many chemical and biological processes
in the environment are affected—
Traditionally, the ecological health of a directly or indirectly—by the physical
marsh has been characterized by characteristics of that environment
measuring changes in its areal extent (Thomann and Mueller 1987).
and the abundance and diversity of its Therefore, collection of physicochemical
data such as salinity, temperature, (Carriker 1967). In the upper
dissolved oxygen, pH, turbidity, Chesapeake Bay, sedimentation,
nutrients, contaminants, and depth stratification, circulation, nutrient levels,
provides information necessary to and dissolved oxygen concentrations are
evaluate biological data. all determined by the strength and
variation of the fresh water inflow from
Although organisms living in estuaries the Susquehanna River.
are adapted for life in a physically
dynamic system, many are living near Basic water quality parameters should
the limit of their physiological tolerance always be monitored to provide a record
range and any long-term alteration of of environmental conditions at the time
physicochemical environmental of sampling and to provide information
conditions could force their permanent used in assessing the condition of
exclusion from the estuary. Even in biological assemblages. These
minimally-impaired estuaries, causes of parameters should be measured at the
mass mortalities have been attributed to same time and location as the biological
depletions of dissolved oxygen and sampling. Such episodic data will only
changes in temperature, salinity, and serve to provide a snapshot of the
excessive turbidity (Odum 1970). In conditions at the time of sampling and
areas subjected to anthropogenic stress, will not characterize the habitat
changes in physical and chemical conditions in such dynamic ecosystems.
parameters may occur too frequently, be To properly characterize many water
increased in magnitude, or be sustained quality conditions, long-term data sets
for periods of time that only the are required, including data collected at
extremely tolerant organisms can short intervals over complete tidal cycles
endure. for each season.
The community composition of marine Monitoring schemes for

and estuarine fish assemblages is physicochemical water quality
determined by the various species characteristics of the habitat usually
tolerances and preferences for involve in situ methods. Data on the
environmental variables such as water column's characteristics can be
substrate, salinity, and temperature collected relatively inexpensively; the
(Weinstein et al. 1980). These expense of different methods is
environmental variables are controlled generally governed by the level of
by the quantity and direction of the flow automation. Nonetheless, it is essential
of water; i.e., fresh water inflow, tidal to standardize the monitoring design in
cycles, circulation patterns, etc. The order to ensure the comparability of
spatial and temporal distribution and monitoring data throughout the
abundance of fishes would typically be program.
determined by these variables.
Anthropogenic stress adds to the Measurements of temperature, salinity,
complexity by interfering with some and turbidity should be taken at a
aspects of the physiology of the fishes. minimum of four depths in the vertical
profile: (1) 1-m below the surface, (2) 1-
In the Chesapeake Bay, salinity is the m above the bottom, (3) 1-m above the
major factor affecting the regional pycnocline, and (4) 1-m below the
distribution of macrobenthos, while pycnocline. If the waters are too
sediment characteristics have the most shallow or no stratification occurs, it
influence over local distributions would be appropriate to take samples

just below the surface, at mid-depth, and The best-known estuarine zonation
just above the bottom. However, system (the Venice system) is based on
features of water masses recorded in the salinity and establishes five estuarine
historical data; i.e., historical profiles of salinity zones:
salinity, temperature, and turbidity, and
the collection of other data types (e.g., < Limnetic (0-0.5-ppt)
plankton community structure and < Oligohaline (0.5-5-ppt)
water chemistry) should be considered < Mesohaline (5-18-ppt)
when establishing sample depths (Pond < Polyhaline (18-30-ppt)
and Pickard 1983). < Euhaline (>30-ppt).
When using in situ methods (e.g., a Bulger et al. (1993) conducted a Principal
conductivity-temperature-depth meter Components Analysis (PCA) to derive
[CTD], temperature, salinity and pH estuarine salinity zones based on field
measurements should be taken at 1-m data on the salinity ranges of 316 species
intervals with a maximum interval of or life stages in the mid-Atlantic region
#5-m in deeper coastal waters. The (primarily species found in the
measurements should be made over the Chesapeake and Delaware Bays). The
entire depth profile (to within 1-m of the PCA showed that the data structure
surface and bottom). Little additional underlying the salinity distributions of
cost is incurred for this detailed the biota could be explained by five
characterization of the water column principal components corresponding to
once the CTD is deployed. In areas of five overlapping salinity zones: 0-4 ppt;
high stratification, a smaller interval 2-14-ppt; 11-18-ppt; 16-27-ppt; and $24-
would be appropriate. With some of the ppt. This zonation scheme is similar to
newer, more expensive probes, a the Venice system, but is objectively
continuous readout is possible and derived from the salinity distribution of
discussion of depth intervals is estuarine organisms. Measurement of
immaterial. the ionic strength of estuarine and
marine waters is typically made using
3.3.1 Salinity salinity. Salinity may be defined as the
total solids in water after all carbonates
Estuaries are transitional zones in which have been converted to oxides, all
the chemical composition varies from bromide and iodide have been replaced
that of freshwater to marine. Salinity is by chloride, and all organic matter has
a key determinant in the distribution of been oxidized (APHA 1981), and is
estuarine flora and fauna, especially for usually reported as grams per kilogram
benthic invertebrate communities (e.g., or parts per thousand. Salinity is most
Engle et al. 1994, Holland et al. 1987, commonly measured electronically
Summers et al. 1993, Weisberg et al. using a salinometer probe as part of a
1993). Taxa richness is most strongly CTD unit.
affected by salinity, with relatively low
richness in brackish waters compared to A related measure of the ionic strength
freshwater and seawater. Taxa richness of water samples is the conductivity,
metrics can be expressed as a "percent of which is the ability of an aqueous
expected" for a given salinity (Engle et solution to carry an electric current.
al. 1994, Summers et al. 1993, Weisberg This ability depends on the presence of
et al. 1993). ions, their total concentration, mobility,
valence, relative concentrations, and on
the temperature of measurement.
Conductivity is a more useful measure air temperature and depth, leading to
in the tidal fresh water portion of vertical temperature gradients.
estuaries than is salinity (or chlorinity).
Conductivity is most frequently In addition to the potential influence of
measured using a CTD meter. natural temperature variations on
aquatic biota and chemical reactions,
The EMAP-Estuaries program collects anthropogenic thermal inputs can lead
point-in-time salinity measurements to significant modifications of estuarine
concurrently with the collection of and coastal marine biological
biological and sediment samples using a communities. A prime example is
CTD probe (Holland 1990). CTD- thermal loading via discharge of cooling
measured salinity is also incorporated in water from power plants and other
other estuarine monitoring programs; industrial facilities. The important
for example, the Chesapeake Bay influence of thermal discharges is
(Holland et al. 1988, 1989), San Francisco recognized in §316 of the CWA, which
Bay (ABAG 1991), and Puget Sound allows USEPA or states to impose
(PSWQA 1988, 1990, 1991). Monitoring effluent limitations on thermal loading
guidance for the National Estuary at point sources to ensure that balanced,
Program (USEPA 1992) and procedural indigenous populations of shellfish, fish,
and monitoring guidance for the CWA and wildlife in and on a water body will
§403 program (USEPA 1994a) both be maintained. Temperature should be
recommend CTD probes as the preferred measured at each sampling site with a
method for collecting salinity data. CTD probe at 1-m intervals from the
surface to within 1-m of the bottom
3.3.2 Temperature concomitantly with the collection of
salinity and DO data. Diel temperature
Temperature is an important measurements may also be needed.
determinant of the rate of chemical
reactions and biological processes. DO 3.3.3 Dissolved Oxygen
saturation is a function of water
temperature. Temperature influences Dissolved oxygen (DO) is a basic
the spatial and seasonal distribution of physiological requirement for nearly all
benthic infauna (Kendall 1983 cited in aquatic biota and for the maintenance of
Dardeau et al. 1992), microbial process balanced populations (exceptions being
rates (Christian 1989), and temporal and anaerobic systems). Most estuarine
spatial distributions of fishes (e.g., populations can tolerate short exposures
Houde and Zastrow 1991). Estuarine to reduced DO concentrations without
water temperature in temperate regions adverse effects. Extended exposures to
is primarily a function of the DO concentrations less than 60% oxygen
temperatures of influent streams, rivers, saturation may result in modified
the ocean, and tidal stage (Reid and behavior, reduced abundance and
Wood 1976). In the sub-tropical productivity, adverse reproductive
estuaries of Florida and Texas, estuarine effects, and mortality (Holland et al.
temperature may be more closely related 1989, Reish and Barnard 1960, Vernberg
to incident sunlight and air temperature. 1972). Low DO conditions can also
Because most estuaries are shallow, increase the vulnerability of benthos to
there can be considerable diurnal and predation as they extend above the
seasonal temperature variation. sediment surface to obtain more oxygen.
Estuarine temperature also varies with Exposure to less than 30% saturation
(~2-mgL-1 ) for 1 to 4 days causes

mortality to most species, especially (i.e., index) period, and to determine if
during summer when metabolic rates the characteristics of exposure to
are high. Some benthic extreme low DO can be predicted from
macroinvertebrate species tolerate low short-term continuous DO records
DO conditions, and prolonged low DO (Holland 1990). Analyses of the data for
concentrations frequently lead to the Virginian Province showed that
changes in the composition of benthic three instantaneous DO profile
macroinvertebrate assemblages in measurements best characterized the
certain areas (Holland et al. 1989). DO status of a site. In contrast, in the
Aquatic biota exposed to low DO may Louisianian Province the minimum DO
be more susceptible to adverse effects of measured over a 24-hour period was
other stressors (e.g., disease, toxic most successful in characterizing both
chemicals, habitat modification) low and high frequency hypoxia sites.
(Holland 1990). These differences have logistical
implications for bioassessment of
Because DO concentration throughout estuarine and coastal marine waters in
the water column can vary widely with that instantaneous DO measurements
tide, time of day, wind patterns, and can be made with CTD meters equipped
biological activity, the EMAP-Estuaries with a DO probe; the 24-hour minimum
program conducted extensive DO measurements require the use of a
comparisons of point-in-time and continuous recording DO meter that
continuous collections of DO data. In must be deployed and subsequently
deeper areas of Chesapeake Bay, within retrieved. Consequently, dissolved
EMAP's Virginian Province, bottom DO oxygen is an important habitat
has a strong tidal signal; high tide parameter, but the manager must
corresponds to lower DO near the exercise care in both sampling design
bottom. Significant serial and data interpretation when attributing
autocorrelation of dissolved oxygen biotic responses to potential hypoxia.
concentration persists for 6 to 8 days,
indicating that consecutive Collection of DO in Tier 1 of these
measurements taken less than 8 days procedures should include an
apart may not be independent (Holland instantaneous measurement at the same
1990). In some EMAP Louisianian stations and times as biological samples
Province estuaries a strong diurnal cycle are collected. Tier 2 should include
with lower DO occurs at night (Stickney measurement of DO in the early
1984, Turner et al. 1987). Low DO in morning at each station as a minimum.
these shallow, often well-mixed Tier 3 should include DO collected along
estuaries may be highly variable both a depth profile from surface to within 1-
spatially and temporally (Sanford et al. m of the bottom at 1-m intervals. For
1990, Schroeder 1979, Rabalais et al. more detailed characterization of DO
1985). These conditions can lead to conditions, particularly at sites which
misclassification of the ecological may undergo hypoxia, recording DO
condition of estuaries with respect to meters may need be deployed in Tier 3.
hypoxia. In any case, as the EMAP experiences
indicate, careful DO profiles should be
Goals of the EMAP analyses comparing established for each region surveyed
DO measurement approaches were to before any presumptions about
determine the best measure for community response are made.
representing DO exposure, to evaluate
the stability of DO over the sampling
3.3.4 pH resuspended from sediments within
estuaries. Turbidity has two primary
Another important indicator of the effects in estuaries. First, light
chemical condition of estuarine and penetration is reduced, which directly
coastal marine waters is pH. In affects primary production and
estuaries, pH will usually be controlled abundance of aquatic macrophytes in
by the mixing of seawater solutes with the estuary. Second, settling of the
those in the fresh water inflow. A major particulate matter can result in
factor influencing the pH of estuarine deposition zones of mud, silt, other
waters is the carbon dioxide solubility, sediments, and detritus. This deposited
which is a function primarily of salinity material can cause changes in the
and secondarily of temperature. composition of benthic invertebrate
Seawater is a very stable buffering assemblages. For example, deposition of
system containing excess bases, notably mud and silt can result in the clogging
boric acid and borate salts, carbonic acid of gills of oysters and other filter-feeding
and carbonate. Surface seawater pH species and a loss of a hard substrate
usually ranges between pH 8.1 and 8.3. required by these species. In coastal
River waters usually contain a lower areas, the deposition of silt in pockets of
concentration of excess bases than uneven sandy bottom contributes to the
seawater; this shifts the carbonate “patchy” distribution of benthic
buffering system toward a higher invertebrate species, especially annelids,
concentration of free carbon dioxide and amphipods, and isopods. Deposited
lower pH in the upper reaches of rivers. material can also contain particle-
Because fresh water inflow to estuaries adsorbed contaminants; this can result
is typically much less buffered than in contaminated sediment "hot spots".
seawater, greater variation in pH is In contrast to these negative effects on
observed in the less saline portions of the benthic invertebrate assemblage,
estuaries than near their mouths. The turbidity can have positive effects on the
range of pH values observed in the fish assemblage by increasing protection
upper reaches of estuaries can be 7.5 - from predators by reduced visibility.
9.0.
Turbidity can be easily assessed (as light
Measurement of pH in estuaries and penetration) using a Secchi disk, which
coastal marine waters can provide an is probably the most widely used
indication of possible pollutant input method for estimating light penetration
(e.g., releases of acids or caustic (USEPA 1992). Secchi disks are easy to
materials) or high concentrations of use, the results are easy to interpret, and
phytoplankton (due to photosynthesis they are suitable for estimating light
and respiration, pH varies inversely attenuation coefficients through the
with the free carbon dioxide water column. Secchi disk
concentration and directly with DO). measurements may vary somewhat
because of interpersonal differences in
3.3.5 Turbidity visual acuity of observers, and,
therefore, caution must be exercised
The major component of turbidity in when comparing Secchi disk readings
estuaries is silt. The volume of silt taken by different investigators.
discharged into estuaries by streams and
rivers varies seasonally, with the If measurement of turbidity per se is
maximum discharge occurring during deemed necessary by a state, it may be
the wettest months. Silt may also be accomplished in situ by using a

transmissometer or turbidimeter as part based on the finding that, under good
of a CTD system. Nephelometry is the growth conditions, algae have a
preferred method for measuring relatively stable N:P atomic ratio of
turbidity because it is more sensitive, about 15-16:1. This ratio is frequently
effective over a wider range of known as the Redfield ratio (Redfield
turbidities, and less sensitive to particle 1958, Correll 1987, Malone et al. 1996).
size variations than other methods The Redfield ratio is an approximation
(USEPA 1992). and can vary depending on the stage of
algal cell division, changes in light
3.3.6 Nutrients intensity or quality, or temperature
(Correll 1987). Even considering these
Nutrient fluxes are central in controlling factors, measurement of nitrogen and
the primary and secondary production phosphorus concentrations in estuarine
of estuaries. Estuarine autotrophs (i.e., and coastal marine waters provides a
algae, diatoms, vascular plants) require useful benchmark for evaluating the
numerous macro- and micronutrients possible effects of increased loadings of
and vitamins, including C, N, P, Si, S, K, these nutrients. Nutrient limitations in
Mg, Na, Ca, Fe, Mn, Zn, Cu, B, Mo, Co, estuarine and coastal marine waters may
V, thiamin, cyanocobalamin, and biotin change seasonally in response to
(Hutchinson 1967 cited in Day et al. temporal variations in nutrient loadings
1989). Higher trophic levels are in the watershed and in hydrologic
influenced indirectly by nutrients patterns. In the Chesapeake Bay,
through their dependence on a phytoplankton appear to be P-limited
phytoplankton food base. Nitrogen, during spring when biomass reaches its
phosphorus, carbon, and silicon (used annual maximum and N-limited during
by diatoms) are the most studied of the summer when phytoplankton growth
nutrients in estuaries and coastal marine rates are highest (Malone et al. 1996). In
waters (Bricker and Stevenson 1996). North Carolina estuaries, N-limitation
This guidance document focuses occurs across a trophic gradient of
particularly on nitrogen and phosphorus highly productive (Pamlico), moderately
as the two key, potentially limiting and productive (Neuse), and less productive
more manageable nutrients for the systems (Beaufort, Morehead City area)
autotrophic assemblages; i.e., (Mallin 1994). Phosphorus may be co-
macrophytes, phytoplankton, to be limiting in some of these areas during
incorporated in bioassessment portions of the year (Mallin 1994). In the
procedures. The measurement of water Florida Keys and adjacent Florida Bay,
column nutrient concentrations in Tiers LaPointe and Clark (1992) determined
2 and 3 will aid in identifying possible that phosphorus is the primary limiting
sources of biological impairment. nutrient, with nitrogen being co-
NOAA maintains a nationwide database limiting. Smith and Hitchcock (1994)
on eutrophication and toxic algae concluded that phosphorus (and silica)
blooms that can be cited to provide potentially limits phytoplankton growth
water column information. in the Louisiana Bight during winter-
spring, particularly at low salinities. In
It is a basic tenet of botany that multiple late summer nitrogen may be limiting in
nutrients are necessary for plant growth, higher salinity waters of the Louisiana
and that a shortage of any single Bight.
nutrient will limit further growth. Thus,
estuaries are sometimes referred to as Nitrogen and phosphorus occur in
“nutrient-limited.” This concept is estuarine and coastal marine waters in
many forms which can be variously and become a source of toxicity to
described in terms of oxidation state, organisms and bioaccumulation to the
phase (solid-liquid-gas), chemical food chain. Contaminant analyses
structure, or analytical method. should be tailored to the types of
Nitrogen forms are the most diverse, substances known or suspected as
with nitrogen compounds ranging from chemicals of potential concern at a site.
to . Dissolved nitrogen Chemical concentrations should be
species that could be incorporated into compared to applicable sediment quality
chemical analyses of this nutrient guidance documents to aid in
include total dissolved N (TDN), and interpretation and to provide an effort-
dissolved inorganic nitrogen (DIN = based assessment method. Results of
+ + ) (LaPointe and any toxicity tests conducted should be
Clark 1992). Nitrate concentrations are compared against results from controls
typically controlled largely by external and against statistical standards to
inputs to estuarine and coastal marine provide relative rankings. Chemical
waters via land runoff. In some areas analyses, toxicity tests, and benthic
(e.g., Chesapeake Bay) atmospheric analyses constitute the sediment quality
deposition may account for an triad, originally proposed by Long and
important fraction of the nitrogen load Chapman (1985).
to the water body (Dickerson 1995,
Boynton et al. 1995). Ammonia The Sediment Quality Triad approach,
concentrations are highest in waters (SQT) (Long and Chapman 1985,
receiving large inputs of sewage (Day et Chapman et al. 1987, Long 1989,
al. 1989). Dissolved organic nitrogen Chapman 1996) can be used to assess
(DON) can be calculated as TDN minus pollution-induced estuarine and coastal
DIN (LaPointe and Clark 1992). marine system degradation (Schlekat et
al. 1994). In an analysis of sediment
Measurements of total dissolved P metals concentrations from 497 sites in
(TDP) and soluble reactive phosphorus Gulf of Mexico estuaries, Summers et al.
(SRP) can be used to estimate dissolved (1996) normalized metals concentrations
organic phosphorus (DOP = TDP - SRP) for extant concentrations of aluminum
(LaPointe and Clark 1992). to identify the concentrations expected
from natural sources versus
3.3.7 Contaminants anthropogenic sources. Krumgalz
(1993) applied a “fingerprints” approach
Measuring organic compounds and to estuarine and coastal marine
metals is particularly important because pollutant source identification. This
of the adverse effects they can have on approach assumes that if anthropogenic
aquatic life and on human health and pollutants in a particular area had
recreation if these contaminants enter originated from the same source, then
the food chain. Sources of organic and pairwise relationships between the
inorganic chemical contaminants concentrations of these pollutants in
include direct release to the water body, sediments from various sampling sites
urban runoff, atmospheric deposition, in the contaminated area would be
industrial and municipal discharges, linear. The correlations between
and upstream runoff (Velinsky et al. pollutants will depend on the origin of
1994, Wade et al. 1994). Organic and the contaminants and on the patterns of
metals contaminants in the water mixing contaminated sediments and
column will usually be adsorbed onto contaminants with “pure” sediment.
sediment particles, settle to the bottom, Thus, the “fingerprints” can be used to

trace the distribution of contaminants laboratory exposures (Chapman et al.
from a source, or conversely, to identify 1988). If possible, historical data should
potential sources. be used to focus the chemical analyses.
3.3.8 Depth Toxicity data can be generated through a

battery of short-term tests performed
Depth characterization is important for under the controlled environment of the
evaluating DO, temperature and salinity laboratory. Amphipod survival tests,
profiles, tidal regime consistency, and which are most frequently used in North
the percent of the water column that is America, are done with exposures to
photic. This may be especially solid-phase sediments and percent
significant in coastal areas where survival is measured after 10-days.
bathymetry changes can be great and These acute tests often are accompanied
other potentially related distinctions by tests of other sediment phases (e.g.,
such as grain size are not as evident. pore waters and solvent extracts) with
sublethal endpoints (Long et al. 1996).
3.4 Bottom Characteristics Data from the tests provide information
for ranking and prioritizing sampling
The SQT approach is generally the most sites according to their potential for
comprehensive assessment of relative causing adverse effects among resident
sediment quality. In this approach data infauna. Confirmation of adverse effects
are collected to determine among the infauna must be done with
concentrations of potentially toxic analyses of samples collected from the
chemicals in sediments, to measure the same locations tested for chemical
relative bioavailability and toxicity of concentrations and toxicity. Measures of
sediment-associated toxicants with species richness, total abundance,
laboratory bioassays, and to identify relative abundance of crustaceans
degradation of resident infauna possibly (particularly infaunal amphipods)
attributable to the contaminants. and/or other relatively sensitive taxa
provide information on the degree to
Chemical data can be generated through which resident biota have been
analyses of the bulk sediments and adversely affected. Chapman (1996)
compared to applicable sediment quality provided useful guidance on the
guidelines (SQGs), proposed or interpretation of the SQT data.
promulgated criteria or standards
wherever they exist, and relevant Measurements of bottom characteristics
sedimentological factors such as grain of estuaries and coastal marine waters
size, total organic carbon, or aluminum. provide important data for interpreting
Data analyses can be conducted to the condition of targeted biological
identify both sites and chemicals of assemblages. Sediment grain size
potential concern. Chemicals of highest influences the spatial distribution of
potential concern are those in which benthic macroinvertebrates and fishes.
SQG or other applicable values were Fine-grained sediments can adsorb
exceeded most frequently and by the contaminants, creating a source of
largest amount. These chemicals also potential impairment to bottom
would be expected to show strong communities. Organic carbon found in
associations with measures of toxicity. these sediments can mediate the
Moreover, chemicals of highest concern concentrations of DO, organic
may be those determined to be contaminants, and metals. Measuring
bioavailable and bioaccumulative in the depth of the sediment oxidation-
reduction potential discontinuity layer 3.4.2 Total Organic Carbon, Total
provides information on aerobic vs. Volatile Solids, and Acid
anaerobic respiration in sediments. Volatile Sulfides
Sediment nutrients such as particulate
nitrogen and phosphorus can be re- Total organic carbon (TOC) and acid
mobilized by physical disturbance or volatile sulfides (AVS) are considered by
changes in the water column chemistry some to be the most important sediment
to become an additional nutrient source properties determining the
leading to potential eutrophication, bioavailability and toxicity of certain
phytoplankton blooms, and hypoxia of organic compounds and trace metals in
estuarine and coastal marine waters. sediments (DiToro et al. 1990, DiToro et
Finally, sediment contaminant al. 1991). The importance of these
measurements can provide insights on factors is based on an equilibrium
factors that might limit biological partitioning approach. This approach
assemblages and lead to potential assumes that the bioavailable fraction of
human health effects. chemicals in sediment is correlated to
that fraction in the porewater rather
3.4.1 Sediment Grain Size than whole sediment concentrations.
Therefore, factors that influence the
The objective of measuring sediment partitioning of compounds between
grain size is to detect and describe sediment and porewater will govern
spatial and temporal changes of the bioavailability. In addition, it is
benthic habitat. The availability of assumed that equilibrium exists among
sediment contaminants is often the phases (hence, the name
correlated with sediment grain size “equilibrium partitioning”). For non-
because more sediment contaminants ionic hydrophobic organic chemicals,
are adsorbed onto small grained the primary factor influencing
sediments due to their greater surface partitioning is TOC; for certain divalent
area. Likewise, grain size information cationic metals; i.e., cadmium, copper,
may explain the temporal and spatial nickel, lead, zinc, an important binding
variability in biological assemblages phase is the acid volatile sulfide fraction.
related to an organism's ability to build The development of sediment quality
tubes, capture food, and escape criteria by USEPA is based on these
predation. Grain size data may be used assumptions and a comparison of
to determine the extent of or recovery predicted porewater concentrations to
from environmental perturbations, to existing water quality criteria (DiToro et
evaluate the condition of benthic al. 1991, Ankley et al. 1996).
habitats, and to assist in providing early
warnings of potential impacts to the Normalization of non-ionic organic
estuarine ecosystem (USEPA 1992). compounds is accomplished by
The most common measurements and calculating chemical concentrations per
classifications of sediment grain size are gram of sediment organic carbon rather
as follows: than per gram of dry sediment. This
approach allows comparisons of the
< clay < 0.004-mm potential bioavailability of non-ionic
< silt 0.004 - 0.064-mm organic compounds across different
< sand 0.064 - 1.0-mm sediment types and can be used to
< gravel > 1.0-mm screen for chemicals of concern. For an
explanation for how to apply this
approach to calculate sediment quality

criteria the reader is referred to DiToro metals performed equally well in
et al. (1991). correctly predicting samples as either
toxic or non-toxic. For an excellent
Although SQGs (Sediment Quality discussion of the applicability,
Guidelines) derived for organic advantages and disadvantages of this
compounds and trace metals reported approach, the reader is referred to
on a dry weight (bulk) basis have been several review papers in Environmental
shown to be reliable and predictive of Toxicology and Chemistry, Volume 15,
both non-toxic and toxic conditions #12.
(Ingersoll et al. 1996, MacDonald et al.
1996, Long et al. 1998a); these values do 3.4.3 Sediment Oxidation-Reduction
not account for the relative Potential
bioavailability of sediment-associated
chemicals. In areas in which high trace There are four oxidation-reduction
metal concentrations are known or (redox) processes related to biological
suspected, or in which SQGs are respiration that occur in benthic
exceeded, further evaluations of sediments. These chemical reactions,
chemical contamination may be aided in which depend on the availability of
subsequent analyses by use of the electron acceptors; i.e., oxygen, nitrate,
simultaneously extracted metals/acid sulfate, and carbonate, stratify the
volatile sulfides (SEM/AVS) tool to sediments into four zones. Oxygen is
provide estimates of bioavailability. the electron acceptor used for aerobic
respiration and is the most important
The AVS normalization approach oxidizing agent at the surface of the
assumes that select trace metals bind to sediments. Nitrate reduction occurs
sediment sulfide, specifically the sulfide between 0- and 4-cm and produces
fraction soluble in cold acid, known as elemental nitrogen. This is followed by
AVS (Allen et al. 1993). The sulfate reduction which produces
bioavailability of trace metals capable of hydrogen sulfide. Carbonate reduction
forming insoluble metal sulfides will be occurs between 10- and 50-cm and
determined by the proportion of these results in the production of methane.
metal ions not bound to sulfide. Hence,
on a molar basis, if the concentration of Aerobic respiration will be the dominant
SEM is less than the molar concentration reaction as long as oxygen is available.
of AVS, all of the metals should The depth at which oxygen is fully
precipitate as metal sulfides and not be depleted and the redox potential goes to
bioavailable. Conversely, if SEM zero has been termed the redox potential
exceeds AVS then free metal ions may discontinuity (RPD) layer (Day et al.
exist in the porewater. This approach 1989). Burrowing organisms oxidize the
appears to work best in situations when sediments and hence will increase the
the ratio of [SEM]/[AVS] is less than 1.0 zone of habitability as reflected in the
or the difference between SEM and AVS depth of the RPD layer. Color changes
concentrations is less than 0.0 (Hansen in the substrate occur as a result of the
et al. 1996). That is, the SEV/AVS tool is oxidation and reduction of metals, such
primarily intended for use as a no- as iron, in the sediments. The upper few
effects tool and caution is advised in centimeters may appear brown from the
using it as a predictor of toxicity or other formation of iron oxides and
effects. Long et al. (1998b) reported that hydroxides, whereas the zone of
the SEM/AVS tool and SQGs based reduction turns gray and eventually
upon bulk sediment chemistry for trace
black in the deeper sediments from the interactions between natural (e.g.,
formation of ferrous sulfide and pyrite. chemical and physical sediment
When examining a cross-section of a characteristics) and anthropogenic
sediment core sample, the RPD layer is factors (e.g., type and volume of
visibly noticeable by this change in contaminant loadings) (Sharpe et al.
color. The depth of this color change 1984).
should be recorded because, as noted
above, it indicates the zone of Bottom sediments in some estuaries
habitability for benthic infauna. The (e.g., harbors near urban areas and
closer to the sediment surface this color industrial centers) are so contaminated
change appears, the less available that they represent a threat to both
dissolved oxygen exists in the sediment human and ecological health (NRC 1989,
porewater. OTA 1987, Weaver 1984), but
contaminated sediments are not limited
3.4.4 Sediment Contamination to these areas. Pollutant runoff from
agricultural areas also is an important
Sampling the surface sediments for the source of contaminant input to estuaries
presence of contaminants can provide (Boynton et al. 1988, Pait et al. 1989).
insight on factors limiting the benthic
community, as well as the potential for The EMAP program uses the NOAA
impacts to human health; i.e., by National Status and Trends (NS&T)
biomagnification or bioaccumulation in suite of contaminants as the basis for
the food chain or by the contamination measurements in homogenized
of shellfish. Metals and organic subsamples of collected sediments
chemicals entering estuaries from fresh (Figure 3-1). A useful citation for the
water inflows, point sources of NS&T Program list of chemicals is
pollution, and various nonpoint sources, O’Connor et al. 1994. The NOAA suite
including atmospheric deposition, includes chlorinated pesticides,
generally are retained within estuaries polychlorinated biphenyls (PCBs),
and accumulate within the sediments polyaromatic hydrocarbons (PAHs),
(Forstner and Wittman 1981, Hinga major elements, and trace metals.
1988, Nixon et al. 1986, Schubel and
Carter 1984, Turekian 1977) because of 3.5 Proposed Habitat
the affinity of most contaminants for Parameters
particle adsorption (Hinga 1988;
Honeyman and Santschi 1988). Table 3-1 summarizes the proposed
Chemical and microbial contaminants habitat measurements by survey tier and
generally adsorb to fine-grained provides possible sources of
materials in the water and are deposited information, methods, and equipment,
on the bottom, accumulating at as appropriate. Agency-specific
deposition sites, including regions of objectives will determine the overall
upper tidal fresh water, low current design of any sampling program. The
velocity, deep basins, and the zone of following tier distribution is just one
maximum turbidity in the upper reaches approach possible for gathering and
of estuaries within which suspended organizing data. Habitat measurements
sediment concentrations are greater than are intended to be cumulative across
those either farther upstream or farther tiers; that is, the desktop screening of
seaward (Schubel and Carter 1984). The Tier 0 should be incorporated into Tier 1,
concentration of contaminants in Tiers 0 and 1 parameters should be
sediments is dependent upon incorporated into Tier 2, and Tiers 0, 1,

Figure 3-1
Polyaromatic Hydrocarbons Chlorinated pesticides other than DDT
(PAHs) Ald rin Chemicals
Alpha-Chlordane measured in
Acenaphthene Trans-Nonachlor sediments by
Anthracene Die ldrin the EMAP-
Benz(a)anthracene Heptachlor Estuaries
Benzo(a)pyrene Heptachlor epoxide program.
Benzo(e)pyrene Hexachlorobenzene Refer also to
Biph enyl Lindane (gamm a-BHC) the NS&T
Chrysene Mirex Program list of
Dibenz(am h)anthracene chemicals
2,6-dimenhyulnaphthalene 18 PCB Congener (O’Connor et
Fluoranthene al. 1994).
Fluorene Congener Location
2-methylnaphthalene Number of CIs
1-methylnaphthalene 8 2 4'
1-methylphenanthrene 18 2 2' 5
Naphthalene 28 2 4 4'
Perylene 52 2 2' 5 5'
Phenanthrene 44 2 2' 3 5'
Pyrene 66 2 3' 4 4'
Benzo(b)fluoranthene 74 2 4 4' 5
Acenaphthlyene 99 2 2' 4 4' 5
Benzo(k)fluoranthene 101 2 2' 4 5 5'
Benzo(g,h,i)perylene
118 2 3' 4 4' 5
153 2 2' 4 4' 5 5'
Major E leme nts
105 2 3 3' 4 4'
Aluminum
138 2 2' 3 4 4' 5'
Iron
187 2 2' 3 4' 5 5' 6
Manganese
128 2 2' 3 3' 4 4'
Silicon
180 2 2' 3 4 4' 5 5'
170 2 2' 3 3' 4 4' 5
Trace E leme nts
195 2 2' 3 3' 4 4' 5 6
Antimony
206 2 2' 3 3' 4 4' 5 5' 6
Arsenic
209 2 2' 3 3' 4 4' 5 5' 6 6'
Cadmium
Chromium
Copper Other m easurements
Lead Tributyltin
Merc ury Acid volatile sulfides
Nickel Total organic carbon
Selenium
Silver
Tin
Zinc
DDT and its metabolites
o,p'-DDD
p,p'-DDD
o,p'-DDE
p,p'-DDE
o,p'-DDT
p,p'-DDT
and 2 parameters should be present. Initial partitioning will
incorporated into Tier 3. The habitat probably be based on salinity, sediment
tiers described here should be used with type, and depth.
the corresponding biological survey tier.
Watershed Land Use and Population
3.5.1 Tier 0
Land use and population data for the
The purpose of a Tier 0 assessment is to watershed will help to identify classes of
support the planning for monitoring and contaminants and other stresses that
more detailed assessments. Tier 0 is a may affect the water body. For example,
desktop screening assessment in which agricultural areas located near an
documented information for the estuary estuary might be expected to be sources
or coastal marine areas of concern is of nonpoint loading of nutrients,
compiled from sources including pesticides, herbicides, and sediment.
databases, peer-reviewed and gray Urban areas may contribute toxic
literature, state and federal agencies, compounds via stormwater runoff. The
universities, and local experts. A Tier 0 pattern and magnitude of population
assessment should always precede any density in the watershed can potentially
of the three subsequent tiers. provide clues regarding the potential for
Examination of long-term data records human-induced impacts to the water
(e.g., salinity, DO, climate) is body.
particularly important for identifying
the variability which must be accounted Water Column and Bottom
for in the design of subsequent field Characteristics
monitoring. Habitat parameters to
examine in Tier 0 include: Historic data on water column and
bottom characteristics is central for
Area and Geomorphometric identifying system variability and to
Classification support the design of subsequent
monitoring. This data can also be used
The size and classification of an estuary by states to identify types and locations
indicates its potential to respond to of potential impairment, for example,
various impacts. Estuary types include areas with high concentrations of water
coastal plain, lagoon, fjord, and column nutrients, suspended sediment,
tectonically-caused. Circulation type or sediment contaminants.
(e.g., gravitational, tidal, wind-induced)
influences current patterns, salinity 3.5.2 Tier 1
regimes, and thermal and dissolved
oxygen patterns. Tier 1 is a basic field assessment that is
used for screening purposes to identify
Habitat Type potential reference and impaired sites.
For biocriteria development purposes, it
Identifying and delineating the various is adequate for only rudimentary habitat
habitat types (Section 3.3) that occur in classifications and evaluations. It
the estuary or coastal marine waters will identifies the general physical
be necessary for partitioning the natural characteristics of the estuary or coastal
variability in the system. The extent of region, the habitats, and the potential
such a delineation will depend on the sources of anthropogenic stress. Tier 1
size of the area of concern and the relies heavily on existing information
nature of the environmental gradients identified in Tier 0 and supplemented

by one-time easily-measured field tidal stage and current velocity at the
parameters, which are measured time of sampling at each station should
concomitantly with the collection of be acquired from NOAA.
biological data. Much of the habitat
information needed in this tier can be Bottom Characteristics
acquired from state or federal agency
records. Depending on the needs of the Characteristics of bottom sediments also
state, Tier 1 habitat characterizations are key determinants of aquatic biota
may include the following elements: present in estuaries and coastal marine
waters. Parameters to be measured in
Estuary Characteristics Tier 1 include depth, dominant sediment
type, total volatile solids, and sediment
Information on estuary characteristics is RPD layer depth.
essential for the development of
appropriate sampling strategies. Data to 3.5.3 Tier 2
be compiled in this category includes
estuary area, geomorphometric Tier 2 provides the information
classification (e.g., classical coastal plain necessary to develop a quantitative
estuary, lagoon), and habitat types ranking of the sites that can be used to
present (e.g., hard bottom, soft bottom). prioritize resources and sampling
These data can be obtained from USGS efforts. Habitat information collected in
maps, NOAA charts, and reports and Tier 2 will be used in the development
data archives at federal and state of biocriteria. In addition to Tier 1
agencies and universities. habitat characterization, Tier 2 includes:
Watershed Characteristics Water Column Nutrients
Knowledge of watershed characteristics Nutrients in the water column

can provide important information for determine the nutrient state of the area
determining appropriate sampling and may indicate possible sources of
station locations and for evaluating impairment, particularly nonpoint
possible sources and causes of biological source runoff.
and habitat impairment. Data to be
compiled for this category include Sediment Characterization
watershed land use, human population
density, NPDES discharge locations, and The organisms closely associated with
vegetative cover. These data are likely the bottom are strongly influenced by
to exist at federal, state, and local such sediment characteristics as the
agencies and universities. average grain size and the percent
composition of silt, sand, and clay (Day
Water Column Characteristics et al. 1989). These characteristics
determine the structure of the benthic
The characteristics in a water column community based on the preferences of
play a key role in determining the biota the major groups of organisms. For
present at a given location and their example, suspension feeders are found
broader distribution patterns. more often in firmer, sandier substrates
Parameters to be measured in Tier 1 in than are deposit feeders; interstitial
the field include salinity and meiofauna are predominant in sandy
conductivity, DO, temperature, pH, areas, whereas burrowing meiofauna
turbidity and Secchi depth. Records of prefer silty mud. Although a high
organic content in the sediments can Program) and can be adapted for use in
increase the rate of oxygen depletion, other areas.
there are many organisms that require
high concentrations of organic matter. 3.5.4 Tier 3
Sediment characteristics to be measured
in Tier 2 include percent sand vs. silt- Tier 3 provides a detailed assessment
clay, mean grain size, total volatile with a high level of certainty of the
solids, and total organic carbon. biological or habitat condition of the
estuarine and coastal marine
Shorezone Vegetative Cover environment. It is the definitive
Characterization assessment level to distinguish habitat
variation from anthropogenic impacts
Shorezone vegetation provides stability when the biocriteria have been
for beaches, wetlands, banks, and cliffs, exceeded. Tier 3 focuses on biological
serving to reduce erosion and nonpoint community level investigations and
source runoff to the water body. As thoroughly integrates the physical,
such, evaluation of shorezone vegetative chemical and biological data to yield a
cover is important for identifying detailed impact assessment. In addition
possible sources of impairment and to the habitat parameters compiled in
remedial approaches. Terrestrial Tier 0 and measured in Tiers 1 and 2,
riparian vegetated areas to consider are sediment oxidation-reduction potential,
uplands and the floodplain. Areas of sand/silt/clay proportions, sediment
emergent, intertidal, and submerged contaminants, and water column
vegetation should also be characterized. pesticides, herbicides, and metals,
nutrient speciation, and AVS/SEM as
Shorezone vegetative cover is important needed may be measured in this tier.
for reducing nutrient and sediment
loading to estuaries from nonpoint Tier 3 provides the detailed diagnostic
source runoff, attenuating incident wave information necessary for: (1)
energy and reducing shore erosion, and identifying specific problem sources in
providing important nursery and the drainage area; (2) delineating
feeding habitat for migratory species. mitigation options for the identified
Salt marshes and aquatic macrophytes problems; and (3) preparing written
have high gross primary productivity management plans for the estuary or
and provide a source of autochthonous coastal marine area of interest.
organic matter for detrital feeders in Although the data collected in Tier 3
adjacent waters. An assessment of the cannot prove cause-and-effect
coverage and types of shorezone relationships between identified
vegetation can contribute to the overall stressors and ecosystem responses, they
assessment of the condition of estuarine can provide a strong correlation and a
and coastal marine habitat. Evaluation definitive assessment, with a high
of vegetative cover is most easily degree of certainty, of the biological
accomplished by aerial photography integrity of the target waters and their
and mapping coupled with ground- habitats.
truthing. Detailed procedures used for
photography and mapping aquatic
macrophytes are provided by Orth et al.
(1993) (Chesapeake Bay), Ferguson and
Wood (1994) (North Carolina estuaries),
and USEPA (1992) (National Estuary

Table 3-1. Habitat measurements for estuaries and coastal marine waters.
Habitat Assessment Tier Information Source Method(s) and

Measurements Equipment
0 1 2 3
Historical Information
Estuary area T T T T USGS quad maps Can be estimated from

maps or using GIS
Geomorphometric T T T T USGS quad maps

classification
(classical coastal
plain estuary; salt
marsh estuary;
lagoon; fjord;
tectonically-caused
estuary)
Habitat type T T T T NOAA bathymetry

(seagrass beds; hard charts; historic surveys
bottom; soft bottom; by federal, state
water column; agencies and
emergent marsh; universities
mudflat; sandflat;
gravel/cobble; rocky)
Watershed land use T T T T USGS land use maps; Can be estimated from
state planning maps or using GIS
agencies; local zoning
agencies
Population density T T T T US census data
NPDES discharges T T T T State water quality

agency
Vegetative cover T T T T Historic surveys by Can be estimated from

federal, state agencies maps or using GIS
and universities
Field-collected Information: Water Column Characteristics
Salinity, conductivity T* T T T Historic data from Conductivity cells

federal, state agencies (CTD meters)
and universities
DO T* T T T Historic data from CTD meter equipped

federal, state agencies with O2 probe,
and universities recording DO meters
for Tier 3 may be
needed
Temperature T* T T T Historic data from CTD meter, satellite

federal, state agencies remote sensing.
and universities
pH T* T T T Historic data from CTD meter equipped

federal, state agencies with pH probe
and universities.
Table 3-1 (Cont’d). Habitat measurements for estuaries and coastal marine waters.
Habitat Assessment Tier Information Source Method(s) and

Measurements Equipment
0 1 2 3
Turbidity, Secchi 7* 7 7 7 Historic data from Secchi disk;

depth federal, state agencies transmissometer,
and universities nephelometer,
turbidimeter if desired
Nutrients (nitrogen 7* 7 7 Historic data from Spectrophotometry

species, federal, state agencies
phosphorus) and universities
Organics, metals 7* 7 Historic data from Standard methods for

federal, state agencies selected suite of
and universities contaminants
Field-collected Information: Bottom Characteristics
Depth 7* 7 7 7 Historic data from Meter wheel,

federal, state agencies fathometer,
and universities hydrostatic pressure
sensor
Sediment grain size 7* 7 7 7 Historic data from Sieving or separatory

federal, state agencies column combined with
and universities pipette analysis for
silt-clay fraction
Total volatile solids 7* 7 7 7 Historic data from Standard methods

federal, state agencies
and universities
Total organic carbon 7* 7 7 Historic data from Standard methods

and universities
Acid volatile sulfides 7* 7 Historic data from Standard methods

and universities
Sediment reduction- 7* 7 7 7 Historic data from Visual determination

oxidation potential federal, state agencies of the depth of change
and universities in sediment color in
core
Sediment 7* 7 Historic data from Standard methods for

contamination federal, state agencies contaminants selected
and universities
* Historic data should be included in Tier 0; the tier does not include any field collection of
new data.

Chapter 4
Physical Classification and
the Biological Reference
Condition
Estuaries and coastal marine waters are minimally impaired by human

span a range of spatial scales from small pollution and disturbance. The care that
subestuaries, embayments, and coastal states use in selecting reference sites and
lagoons to large estuaries (e.g., developing reference condition
Chesapeake Bay, Puget Sound) and parameters, together with their use of
open coastal waters. The procedures standardized survey techniques, will
described in this document rely on a directly influence the quality of the
spatial hierarchy to accommodate the resulting water body assessment. At a
potentially large range of water bodies minimum, reference conditions should
that states may assess. The top level in be identified for each of the estuary and
the hierarchy is a geographic region coastal marine classification categories
containing comparable landform and developed by a state.
climate. The provinces used by the
EMAP-Estuaries program (e.g., Reference conditions reflect the biotic
Carolinian, Columbian) are examples of potential for estuaries and coastal
this hierarchical level. The next level marine waters if they are not impaired
consists of individual watershed by human activity or pollution.
characteristics. Key attributes to Attainment of an aquatic life designated
consider at this level include land cover, use is evaluated against the reference
the watershed-to-basin area ratio, and condition as a key element in the
the geology and soils of the watershed. biocriteria for that aquatic life use.
Examples of the use of this hierarchical Biocriteria may be set higher than the
level in estuarine assessment are the best conditions observed in the data
Chesapeake Bay watershed, New Jersey available for an area that is highly
coastal bays, or California saline impaired. In this instance, interim,
lagoons. The lowest level in the incremental criteria may be established
hierarchy considers habitat as the regional authority works on
characteristics. As discussed in Chapter environmental recovery.
3, the three primary variables used to
partition spatial heterogeneity at this 4.1 Classification Approach
level are sediment grain size, salinity,
and water depth. Description of The biological reference condition must
sampling sites as “low mesohaline, be determined separately for each
mud” or “10-m depth, gravel” would be estuarine or coastal marine physical
examples of this level of the hierarchy. class. Assessing biological condition
requires reference conditions for
Reference conditions are expectations of comparison and for development of
the status of biological communities in models and indexes to help establish
the absence of anthropogenic biocriteria and detect impairment.
disturbances and pollution, and are There is no single "best" classification
usually based on the status of multiple nor are resources available to determine
reference sites. Ideally, reference sites all possible differences between all
estuarine and coastal marine sites in a applies to all estuaries (or coastal marine
region. The key to classification is waters) would be inappropriate. The
practicality within the region or state in purpose of classification is to group
which it will be applied; i.e., local similar estuarine or coastal marine sites
conditions determine the classes. together; i.e., to prevent the comparison
Classification will depend on regional of apples and oranges. Classifying the
experts familiar with the range of variability of biological measures within
estuarine conditions in a region as well groups inevitably requires professional
as the biological similarities and judgment to arrive at a workable system
differences among the assessment units. that separates clearly different systems,
Ultimately, physical classification may does not consider each estuary or
be used to develop a predictive model of subestuary a special case, and does not
those estuarine and coastal marine lead to the proliferation of classification
characteristics that affect the values of groups. The intent of classification is to
the biological metrics and indexes at identify the smallest number of groups
reference sites. of estuarine or coastal marine categories
that under ideal conditions would have
The regional differences in estuarine and comparable biological communities for
coastal marine biological communities that region. As much as possible,
across the United States must be classification should be restricted to
accounted for in the development of a those characteristics of estuaries and
biological criteria program. These coastal marine waters that are intrinsic,
differences can be identified by natural, reasonably stable over time, and
comparing the biology of water bodies not the result of human activities.
of interest to a reference condition. As
biological conditions change across the The approach to reference condition
country, the reference conditions will characterization and classification is
also change. To account for the regional illustrated in Figure 4-1. An idealized
geographic differences that create biological potential for estuarine sites is
structural differences in biological expressed, for instance, by a fish index
habitat (either natural or human- and an infaunal index, each within a
induced), states should classify estuaries certain range of values (Figure 4-1). A
and coastal marine waters or segments test site is compared to the expected
thereof into groups. A reference ranges of values, and if its indexes are
condition should be established for each outside those ranges, it is judged as not
of these classification groups. Biotic meeting expectations to some degree.
index comparisons can then be made Test sites are usually not compared to a
within each classification group and theoretical ideal, but to biological
inappropriate biological comparisons criteria derived from a population of
between different classes will be reference sites. Test sites are judged as
precluded. Moreover, the aquatic life not meeting the criterion if they are
expectations of water bodies are beyond some predetermined limit of the
tempered by realistic expectations. With distribution of reference values.
biological systems, it is not possible to
set uniform, nationwide numeric
biological criteria.
Estuaries vary widely in size, shape, and

ecological and physical characteristics,
and a single reference condition that
4-2 Physical Classification and the Biological Reference Condition

Figure 4-1
4 Graphical
representation of
bioassessment.
Assessment sites
a and b are
3 compared to an
ideal biological
2.0 - 2.7 potential. Site a is
"Biological Potential" near its potential.
Site a
Fish Index
Site b deviates
2 from it.
1.7 - 3.3
Site b
0
0 1 2 3 4
Infaunal Index
A population of reference sites might Sequence of Classification and

consist of sites which overlap different Characterization
classes of estuarine or coastal marine
waters (Figure 4-2). A useful The general sequence of reference
classification system in this instance condition characterization is to first
separates these reference sites into make a preliminary physical
classes with different biological classification of estuaries and coastal
expectations. The classification itself
marine areas within a region (Conquest
must be based on abiotic information
et al. 1994). Because of natural variation
that is minimally affected by human
among and within estuaries and coastal
activities (e.g., ecoregion, estuary and
coastal marine physical characteristics, marine waters, reference conditions will
basin characteristics), such that test sites likely differ with geographic regions,
can be assigned to one of the classes major salinity zones, depth profiles, and
before any biological information is bottom sediment types. Following
obtained. Furthermore, the classification, reference conditions are
classification must explain biological characterized using some combination
variability in the reference sites (Figure of reference sites, historical data, expert
4-2). Separation into classes then lowers opinion, and empirical models. A key
inherent variation and allows greater element is the use of reference sites
precision in assessing test sites. If test because they represent realistic,
site "a" in Figure 4-2 is a member of class achievable goals and can be regularly
II, it would be judged as not meeting monitored. Historical data and well-
reference expectations. If, however, the documented expert opinion should be
physical classification were not done, used to evaluate the information
site "a" would be judged to meet developed from the reference site data
reference expectations because it is
and possibly from empirical models.
within the limits of all reference sites.
The preliminary classification is
reconciled with the biological data to
Figure 4-2
2
Classification and
assessment. If
reference sites are
not classified, Site
a is at or near its 1
potential. If
reference sites are
Fish Index
classified and Site
a is in Class II, it 0
Class I
does not meet its
Class II
potential and Site a
might be judged
impaired.
-1
-2
-1.5 -1.0 -0.5 0.0 0.5 1.0 1.5
Infaunal Index
ensure that the final classification is geographic regions and then to increase
meaningful and the reference conditions the stratification in the classification
are properly characterized. The hierarchy to a reasonable point for each
remaining sections of this chapter cover given region. Although several possible
physical classification, elements of classification levels are outlined below,
reference condition characterization, and in practice, one to three relevant levels
use of reference sites. The reference site would be entirely sufficient.
database should be periodically Classification should avoid a
reviewed as data accumulate to ensure proliferation of classes that do not
consistency of the reference contribute to assessment. The proposed
characterization and classification hierarchical scheme below applies to
scheme. both estuarine and coastal marine
waters.
4.2 Physical Classification
4.2.1 Geographic Region
This protocol is not intended to develop
a classification scheme applicable to the The geographic region, be it ecoregion,
entire United States. Classification physiographic province or other
within the broad estuarine categories delineation, determines landscape-level
described in Section 3.1 must be features for classification such as:
regional, and regional expertise must be climate, topography, regional geology
used to determine those classification and soils, biogeography, and broad land
variables which are useful in each use patterns. Ecoregions are based on
region. geology, soils, geomorphology,
dominant land uses, and natural
A useful classification scheme is vegetation (Hughes and Larsen 1988,
hierarchical, beginning at the highest Omernik 1987) and have been shown to
(regional) level and stratifying only as account for the variability of water
far down as necessary (Conquest et al. quality and aquatic biota in several
1994). The procedure is to classify freshwater areas of the United States.
estuaries and coastal marine waters by Seventy-six ecoregions were originally

identified in the conterminous United make initial divisions of estuaries on a
States (Omernik 1987); but recent regional scale.
refinements have yielded a greater
resolution for some areas. There are two types of coastal plain
estuaries: classical and salt marsh. The
It should be noted that many of the classical coastal plain estuary is
characteristics that can be used as sometimes referred to as a "drowned
classification variables are often river valley." These estuaries were
subsumed by the geographic region. For formed during the last eustatic rise in
example, watersheds are often similar sea level and they exhibit
within major geographic regions, having geomorphological features similar to
resulted from the regional river channels and floodplains. The salt
geomorphology. Within such regions, it marsh estuary lacks a major river source
might be sufficient to classify using only and is characterized by a well-defined
morphology such as depth, area, or tidal drainage network, dendritically
bathymetry. Examples are the coastal intersecting the extensive coastal salt
bays of the Delmarva peninsula or the marshes (Day et al. 1989). Exchange
sounds behind North Carolina's Outer with the ocean occurs through narrow
Banks. tidal inlets which are in a constant state
of flux. Consequently, salt marsh
The EMAP-Estuaries program uses estuarine circulation is dominated by
biogeograpical provinces, defined by: fresh water inflow and the tides.
major climatic zones and prevailing
ocean currents. EMAP coastal areas in Lagoons are characterized by narrow
the continental United States are tidal inlets and uniformly shallow; i.e.,
encompassed within seven provinces less than 2-m deep, open water areas.
described as Acadian, Virginian, The inlets are created by the erosion of
Carolinian; West Indian; Louisianian; the narrow Pleistocene ridge that
Californian; and Columbian (Figure 4-3) formed along the coast some 80,000
(Holland 1990). These roughly years ago during the interglacial stage
approximate the traditional descriptors (Day et al. 1989). Lagoons are primarily
of New England, Mid-Atlantic Bight, wind-dominated and they have a
Southeast Coastal, Caribbean, Gulf subaqueous drainage channel network
Coastal, Southwest, and Northwest that is not as well-drained as the salt
Pacific Coast. For strictly coastal waters, marsh estuary.
this may be a sufficient level of
classification. Classical fjords, formed during the last
ice age, are river valleys that were
4.2.2 Estuarine Categories carved out by the leading ice edge of
advancing continental glaciers. When
Estuaries can be categorized into four the glacier receded, large rock deposits
major classes based on their were left behind where the leading edge
geomorphology: (1) coastal plain had stopped. Others are also a result of
estuaries (Chesapeake Bay; Cape glacial scouring of the coast; however,
Canaveral, FL), (2) lagoons (Pamlico these estuaries were formed in regions
Sound, NC), (3) fjords (Puget Sound), with less spectacular continental relief
and (4) tectonically-caused estuaries and more extensive continental shelves,
(San Francisco Bay) (Day et al. 1989). therefore they are much shallower than
While these classifications appear to be typical fjords.
large scale in nature, they can be used to
Figure 4-3
Biogeographical Columbian
provinces adapted
from Holland
Acadian
(1990). A form of
preliminary
regionalization
used by EMAP- Virginian
Estuaries.
Californian
Carolinian
Louisianian
Arctic West Indian
Bering
Insular
Aleutian Alaskan
Tectonically-caused estuaries are created 4.2.4 Waterbody Characteristics

by faulting, graben formation, landslide,
or volcanic eruption. They are highly The third level of the classification
variable and they may resemble coastal hierarchy focuses on waterbody
plain estuaries, lagoons, or fjords. characteristics. Attributes that are
considered at this level include
4.2.3 Watershed Characteristics waterbody morphology,
hydrodynamics, and water quality.
Watershed characteristics affect estuary Each of these factors has a direct
and coastal marine hydrodynamics, influence on the biota present in the
sediment and nutrient loads, chemical waterbody.
and metals contaminant loads, and
dissolved solids. Watershed Morphological Characteristics
characteristics that may be used as
classification variables include: Morphological characteristics of the
estuary or coastal marine waters
< Land cover - extent of natural influence hydrodynamics and system
vegetation; responses to pollution. Morphological
characteristics include:
< Watershed-to-estuary area ratio;
< Depth (mean, maximum);
< Soils, geology (erosiveness of soils),
and topography. < Bathymetry - three-dimensional
bottom profile;
< Surface area;

< Bottom type and sediments - < pH.
substrate and grain size.
Human actions (e.g., discharges, land
Hydrodynamics use, freshwater flow diversions) alter
water quality, especially sediment and
Hydrodynamics forms a basis for water nutrient concentrations, but they can
quality. Mixing and circulation patterns also affect salinity, conductivity,
influence nutrient retention and the turbidity, DO, and pH. Therefore, care
development of hypoxia. must be taken that classification
according to characteristic water quality
Hydrodynamic factors include: reflects natural conditions and not
anthropogenic impacts. For example, if
< Retention time; estuarine sites are highly turbid due to
poor land management practices in the
< Stratification and mixing; watershed, they should not be classified
as highly turbid. Instead, they should
< Currents - speed and direction; be classified according to the turbidity
class they would have had in the
< Tidal range; absence of poor land use.
< Altered inflow to the waterbody, 4.3 Establishing Biological

such as increased or decreased Reference Conditions
freshwater inflow from runoff or
diversions. Estuarine and coastal marine reference
conditions should be established using
Water Quality some combination of four elements: (1)
evaluation of historical data; (2)
As noted above, many water quality sampling of reference sites; (3)
characteristics are relatively uniform prediction of expected conditions using
within a region because they are the models; and (4) expert consensus. Each
result of common regional, watershed, element has its inherent strengths and
and hydrodynamic characteristics. weaknesses (Table 4-1) that states must
Although water quality variables might consider relative to their program needs,
be redundant for a classification scheme available data, and staff expertise.
if regions are the primary classification
variable, it is frequently convenient to 4.3.1 Historical Data
subclassify according to water quality.
An example is the practice of sub- In many cases, historical data are
dividing estuaries along their gradient available that describe past biological
into oligohaline, mesohaline, and conditions in the region. For the
polyhaline regions (see Figure 4-4 for an purpose of this document, historical
example of such a delineation). Water data are datasets collected by programs
quality variables useful for classification that are no longer active; in many cases
are: using methods now superseded by other
methods. Careful evaluation of these
< Salinity and conductivity; data provides insight about past and
potential community composition of
< Turbidity (Secchi depth); estuarine and coastal marine waters and
is an important initial phase in the
< Dissolved oxygen (DO); biocriteria development process.
Figure 4-4 Wet Season/High Flow
Estuarine and
coastal marine
biocriteria survey
method useful for Oligohaline
stratified random
(population
distribution)
reference site
selection. Wet
season/high flow
salinity pattern Mesohaline
showing mainstem
sampling sites for
four salinity and
three substrate
classifications.
Polyhaline
Key
mud
transitional
sand
Marine
coastal land area
single comprehensive
survey site
Review of historical data collected in information alone should not be used to

these waters is helpful for establishing establish precise reference conditions.
potential sample sizes based on the
variability in the record. These records 4.3.2 Reference Sites
are usually available in the published
literature, natural history museums, Reference sites refer to locations within
college and university departments, and a classification category at which data
federal and state agencies. Caution are collected to represent the most
should be exercised in using this
natural ambient conditions present. The
information because some biological
biocriteria approach generally uses this
surveys occurred at impaired sites, may
have used incompatible sampling population of reference sites to establish
methods, inappropriate or inadequate the collective reference condition that
QA/QC procedures, were insufficiently will in turn be used for comparisons of
documented, or had objectives markedly metrics and test sites. Reference sites in
different from biocriteria determination. estuaries and coastal marine waters
While important for establishing include either sites that are distant from
perspective with respect to current point and nonpoint sources and may be
reference site data, historical applied to a variety of test sites in a
given area, or sites that occur along

Table 4-1. Comparison of elements for characterizing reference conditions (adapted from
USEPA 1998b).
Historical Data Present-Day

Predictive Models Expert Consensus
Biology
Yields actual Yields obtainable, When sufficient Relatively inexpensive.

historical best present status. data are not
information on available. Can be better applied
Strengths
status. to biological
Any assemblages or assemblages than
Inexpensive to communities Work well for water models.
obtain. deemed important quality.
can be used. Common sense and
experience can be
incorporated.
Data might be Even best sites Community and May be qualitative

limited. subject to human ecosystem models descriptions of "ideal"
impacts. not always reliable. communities.
Studies likely
were designed Degraded sites might Extrapolation Experts might be
Weaknesses
for different lower subsequent beyond known data biased.

purposes; data biocriteria. and relationships is
might be risky.
inappropriate.
Can be expensive.
Human impacts
present in
historical times
were
sometimes
severe.
gradients of impact; i.e., nearfield/ models) describe observed relationships

farfield. among measured attributes of a system.
This approach models data without
All monitoring sites, whether reference attention to causal factors. Prediction,
or test, can vary spatially and including forecasting and managing, is
temporally due to natural causes. A the primary goal of a descriptive model,
central measure from several reference and the model is considered successful if
sites is used so that natural variability it fits the data well. The utility of
and uncertainty can be accommodated. descriptive models is often affected by
Statistically, this means that the status of the quantity and quality of data
particular estuarine or coastal marine available, and in many cases, insufficient
“test” sites are judged by comparing data exists to construct a useful model.
them to a population of reference sites
for the particular classification category. Mechanistic models seek to explain
There are 3 approaches for using observed relationships as the result of
reference sites; these are discussed in underlying processes - they are also
Section 4.4. called process models. They typically
consist of a set of state variables, which
4.3.3 Models describe how the system is "now", and a
set of dynamic equations that describe
Mathematical models may be how the state variables change over time
characterized as descriptive or (exogenous variables, or "forcing
mechanistic. Descriptive models (also functions" may also be included). In a
known as correlative or statistical sense, mechanistic models are a set of
descriptive models for each component estimate many quantitative or unknown
of a system. The objective of details, and often assumptions about the
mechanistic models is to describe the interaction of system components
system itself and not simply the data represent hypotheses rather than
obtained by taking measurements; i.e., empirically-derived relationships.
"fitting the data" is not the prime Theoretical models can apply to many
objective. Mechanistic models have qualitatively similar systems; they are
many more constraints and are more useful whenever the phenomenon of
time-consuming to construct than interest occurs across multiple systems.
descriptive models due to the need to
match system structure. Despite the fact The degree of complexity of mechanistic
that these models are not designed for models to predict reference conditions is
prediction, they are often built and used potentially unlimited with attendant
to forecast and manage ecological increased costs and loss of predictive
resources for the following reasons: 1) ability as complexity increases (Peters
in some cases, one does not want to 1991). However, these models can
perform an experiment without a provide much insight into the
reasonable idea of what will happen interactions which determine ecological
(e.g. work involving endangered condition. Management-oriented
species); 2) some experiments are not mechanistic models sacrifice numerical
feasible - the amount of data needed for accuracy in order to capture system
a multivariate statistical model grows dynamics. These models are
very rapidly with the number of mathematically complex and require
variables, and obtaining the data more time and effort to develop than
required for a descriptive model is descriptive models. The primary value
prohibitively expensive. of mechanistic models may be for
understanding ecosystem processes and
There are two main types of mechanistic evaluating likely system responses when
models commonly used in biology and mitigation projects are implemented.
ecology. Simulation (also known as
management) models are practically 4.3.4 Expert Opinion/Consensus
oriented and focus on prediction and
management. In these models, In any data evaluation, it is important to
numerical accuracy is what matters establish a qualified team of regional
most, the model need not match the specialists so the error inherent in
system processes and structure. professional judgment can be reduced.
Management models are system specific, This team should evaluate the historical
resulting in numerical predictions for data, the candidate reference sites,
one particular system. Theoretical (also subsequent data collected, and any
known as analytical) models focus on models used in the process. This expert
scientific understanding of the system. team function is even more important
These models are highly analytical, when no candidate reference sites are
typically involving systems of acceptable. Expert consensus then
differential equations, and emphasize becomes a workable alternative in
principles rather than numerical establishing reference expectations.
accuracy. These models have to be Under such circumstances, the reference
simple enough to allow understanding condition may be defined using a
of system behavior and what the model consensus of expert opinion based on
is predicting. This trade-off often sound ecological principles applicable to
requires that the investigator omit or the region of interest.

Three or four biologists are convened for detrimental, such as pollutant inputs, or
each assemblage to be used in the positive, such as responsible resource
assessment, and each expert should be protection or restoration. In either case,
familiar with the estuaries or coastal the manager developing a biocriteria
marine waters and assemblages of the program must evaluate the effect of such
region. The experts are asked to develop activities on biological resources and
a description of the assemblage in habitat. In practice, most reference sites
relatively unimpaired estuaries and will have some of these impacts,
coastal marine waters, based on their however, the selection of reference sites
collective experience. The description is always made from those with the least
developed by consensus will necessarily anthropogenic influences.
be more qualitative than quantitative,
but metrics and metric scoring can be Reference sites must be carefully
developed. selected because they are used as a key
part of the biocriteria benchmark against
It is important that the process used to which test sites are compared. The
review the available information and to conditions at reference sites should
develop a consensus be thoroughly represent the best range of minimally
documented so that it can be repeated in impaired conditions that can be
the future if necessary and to provide achieved within a classification category
quality control on its results. This same for the region. Two primary
panel of biologists and natural resource considerations guide the selection of
managers may also be consulted in the reference sites within each site class:
development of the overall reference minimal impairment and
condition and subsequent biocriteria. In representativeness.
establishing the team of experts, it
should be recognized that bias toward Minimal Impairment - Sites that are
specific assemblages may exist and the relatively undisturbed by human
team should be appropriately balanced. activities are ideal reference sites.
However, land use practices and the
4.4 Use of Reference Sites to presence of major urban areas in the
basins of many of the nation's estuaries
Characterize Reference
or adjacent to its coastal marine waters
Condition have altered the landscape and quality
of water resources to such a degree that
The determination of the biological
truly undisturbed sites are rarely
reference condition from reference sites
available. In fact, it can be argued that
is based on the premise that estuaries
no unimpaired sites exist. Therefore, a
and coastal marine waters least affected
criterion of "minimally impaired" must
by human activity will exhibit biological
be used to determine the selection of
conditions most natural and attainable
reference sites. In regions where
for those waters in the region.
minimally impaired sites are still
Anthropogenic effects include all
significantly degraded, the search for
possible human influences, for example,
suitable sites should be extended over a
watershed disturbances, habitat
wider area, and multistate cooperation
alteration (channel dredging and
may be essential. It is advisable that the
dredged material disposal, shoreline
state make every effort, once reference
bulkheading), nonpoint source inputs,
sites are selected, to protect these areas
point source discharges, atmospheric
from degradation. This may involve:
deposition, and fishing pressure.
purchase of land or easements; where
Human activities can be either
appropriate, location within public reference sites must be physical or
reserves; use restrictions or permit chemical; for example, minimal
constraints on fishing, discharge, or instances of hypoxia, substantially free
dredging/disposal to protect the quality of contaminants, a large proportion of
of the reference area waters. natural vegetation in the watershed,
little or no industrial point sources, little
Representativeness - Reference sites must or no urban runoff, or little or no
be representative of the best quality of agricultural nonpoint source pollution.
the estuaries and coastal marine waters Impaired (“test”) sites for testing
under investigation; that is, they must response of metrics and model building
exhibit conditions similar to what would are selected for the presence of one or
be expected to be found in the region. more such anthropogenic disturbances.
They should not represent degraded Prior definition and selection of
conditions, even if such conditions are reference sites has been used
the most common. Sites containing successfully in streams for fish and
locally unusual environmental invertebrate indexes and models (e.g.,
characteristics can result in Barbour et al. 1995, Ohio EPA 1987,
uncharacteristic biological conditions Reynoldson and Zarull 1993, USEPA
and should be avoided. 1987, Wright et al. 1984), and in estuaries
for benthic invertebrate indexes (Engle
Once the physical estuarine or coastal et al. 1994, Summers et al. 1993,
marine classification is completed, the Weisberg et al. 1993).
biological reference condition should be
defined for each class. This can be Reference Site Criteria - The overall goal
accomplished with three basic in establishing the reference condition
approaches: (1) selected reference sites; from carefully selected reference sites is
(2) determination from population to describe the optimal biota that
distributions; and (3) site-specific investigators may expect to find at the
reference sites. The second approach, test sites of interest in the absence of
determination from population stresses. These "test" or "assessment"
distributions, is a relaxation of the sites can then be compared to the
requirement for minimal impairment; reference sites to determine whether
and the third approach, site-specific impairment exists. The characteristics of
reference sites, is a relaxation of the appropriate reference sites vary among
representativeness requirement. regions of the country and for different
water body and habitat types. In
4.4.1 Selected Reference Sites general, the following characteristics
(modified from Hughes et al. 1986) are
In this approach, reference conditions typical of ideal reference sites:
are characterized based on the best
available sites for a given physical class < Sediments and water column
of estuarine or coastal marine waters, substantially free of contaminants;
and indexes or models are developed by
comparing the best sites (the reference < Natural bathymetry, typical of the
sites) to a second set of sites that may be region;
impaired. The approach assumes that
within the population of sites some are < Natural currents and tidal regime;
minimally disturbed and therefore
comprise a minimally impaired < Shorelines representative of
biological condition. Selection of undisturbed estuaries and coastal

marine areas in the region (generally by sampling a set of stressed sites in the
covered by vegetation with little same way as the reference sites. Sites
evidence of shoreline erosion); with known problems, such as nutrient
loading, thermal pollution, toxic
< Natural color and odor of the water. sediments, or those influenced by urban
land use, are good candidates. There
In this approach, a single minimally should be several in each class for
impaired site does not represent any one adequate tests of metric responses.
region or population of sites, and a Since impaired sites are frequently
frequent difficulty is matching habitats locations of monitoring by water quality
for valid comparison, particularly given agencies, data might already exist to test
that the influence of nonpoint source the biological metrics. However, the
runoff or specific point source sampling methods for reference and
discharges may extend over wide areas impaired sites should be comparable.
due to transport of pollutant loads by
currents and tides. Reference conditions For a lengthy sampling season, it is
based on multiple sites are more important to account for seasonal shifts
representative and are important to of the salinity zone boundaries. Stations
establishing quantitative-based or proximal to these transition zones may
numeric biocriteria. need to be either located far enough
away from the boundary to have
Representative reference sites should be consistent year-round application or else
selected within each of the identified their classification should be shifted
classes. A sufficient number of sites are with the seasons. For example, some
then sampled to adequately characterize areas in Figure 4-5 may be polyhaline-
the range of existing conditions and to sandy bottom in the spring, but in the
reduce the variability in the winter they would be classified as
measurements for each class. It is marine-sandy bottom (Figure 4-6).
desirable to sample a minimum of 10 Thus, such stations have a change of
sites per class, and 30 sites per class is classification with the shifting of the
usually optimal for cost effectiveness. In halocline. An alternative is to avoid
regions where all sites are impacted, the placing stations near the transition zone
selected number of "best" sites of each so that, except in extreme climatic
class (e.g., mesohaline mud habitat) are conditions, these stations have
sampled, where "best" is determined by consistent habitat characteristics. The
least anthropogenic disturbance or biotic data collected at all sites is then
impacts, but not by most desirable biota. subclassified by sediment type (e.g.,
In regions where the population of sand, sandy-mud, mud) and depth for
minimally impaired reference sites is this salinity region. This information
large, a stratified random sampling becomes the reference condition and
scheme (using those sites) will yield an part of the biocriteria for any test sites in
unbiased estimation of reference the region.
conditions (Gilbert 1987).
Example: EMAP Estuary - The EMAP-
Stressed Sites - Effective metrics respond Estuaries (EMAP-E) program collected
to environmental degradation and allow samples in the Virginian and
discrimination of impaired sites from Louisianian provinces. One of the goals
the reference expectations. Metrics that of the EMAP-E effort is to develop a
do not respond are not useful in statistical benthic index of estuarine
bioassessment. Response is determined condition based on extensive
Figure 4-5 Wet Season/High Flow
Estuarine and
coastal marine
biocriteria survey
method useful for Oligohaline
a priori reference
site selection.
Wet season/high
flow salinity
pattern showing
tributary reference tributary
survey
sites and site
mainstem Mesohaline
transects for four
salinity and three
substrate
classifications.
area too
developed for a
reference transect
Polyhaline
Key
mud
transitional
sand NPS loading
Marine
coastal land area
A
survey site
survey site transect
across depth profile
urban areas
agricultural areas
information about benthic community < No sediment toxicity was observed;

structure. A test data set of reference i.e., percent survival greater than
stations has been compiled for the 75% and not significantly different
purpose of formulating the index. from controls;
Habitat characteristics used by EMAP to < Bottom DO was never less than 1-
define reference stations from the 1990 mgL-1, 90% of the continuous DO
and 1991 Virginian province (refer to measurements were greater than 3-
Figure 4-3) collections in Chesapeake mgL-1 and 75% of the DO
Bay were: measurements were greater than 4-
mgL-1 (Schimmel et al. 1994).
< Stations where no contaminant
exceeded the effects range-median The list of stations generated using these
(ER-M) value (which equals the characteristics was reviewed to
concentration at which 50% of eliminate any reference sites located in
collected data demonstrated adverse areas potentially subject to physical
biological effects [Long et al. 1995]); disturbance, such as dredged shipping
channels. Fifty-three sites from the

Dry Season/Low Flow Figure 4-6
Estuarine and
coastal marine
biocriteria survey
Oligohaline method useful for
a priori reference
site selection.
Dry season/low
flow salinity
pattern showing
tributary tributary
survey
site
reference sites
Mesohaline and mainstem
transects for four
salinity and three
substrate
classifications.
area too
developed for a
reference transect
Polyhaline
Key
mud
transitional
sand NPS loading
Marine
coastal land area
A
survey site
survey site transect
across depth profile
urban areas
agricultural areas
combined 1990 and 1991 data sets were < The percent survival for Ampelisca
considered to be reference sites. abdita (10-day) or Mysidopsis bahia
(96-hour) in acute sediment
A similar process has been used for data bioassays was indistinguishable
collected in 1991 in the Louisianian from controls (Engle et al. 1994).
province (refer to Figure 4-3). Using the
following criteria, eight sites were As states develop their estuarine and
classified as reference sites: coastal marine biocriteria, they may
wish to consider incorporating EMAP-
identified reference sites into their
< The minimum DO value over a 24- sampling programs. To the degree that
hour period was less than 3.0-mgL-1 these stations meet state reference
(Summers and Engle 1993); condition requirements, they can serve
as regional reference sites within the
appropriate state classification
< Sediment concentrations for any
categories while also contributing to
contaminant did not exceed the ER-
USEPA national trend monitoring for
M value; estuaries.
4.4.2 Reference Condition Derived Continual monitoring should provide
from Population Distribution the feedback necessary to make
reference condition and interim criteria
One problem in the use of the minimally adjustments as warranted during the
impaired sites technique is what to do if restoration process.
an area is so extensively degraded that
even the least impaired site indicates In this approach, reference conditions
significant deterioration. Many systems are derived from the distribution of
are greatly altered through channel calculated metrics for the entire
dredging and spoil disposal, biological data set within a physical
urbanization, and construction and classification without preselecting any
operation of marinas and other reference sites. The entire data set can
commercial or industrial enterprises. be plotted as a cumulative frequency
The condition of these systems is a result distribution to help determine “best”
of societal decisions that have to be values of candidate metrics (Figure 4-7).
taken into account. However, the This approach is applied in cases where
existence of greatly altered systems prior definition of reference sites is not
should not compromise the objective of possible because all sites are considered
defining the natural state as a reference impaired or because too few reference
condition. These disturbed systems sites exist (e.g., one or two) for an
should not be presumed to represent a unbiased characterization of regional
reference condition of any sort. reference conditions. This approach has
been used successfully for fish and
Although the biocriteria established for invertebrate indexes in streams (e.g.,
these altered systems serve as a baseline Karr et al. 1986, Plafkin et al. 1989) and
for judging impairment, the ultimate for fish (Jordan et al. 1992, Deegan et al.
goal is to achieve the sites' recovery to 1997) in estuaries.
the best attainable condition as
represented by historical information The biological reference condition is
and by conditions at "minimally defined from some upper fraction of the
impaired" sites. Consensus of expert component indicator variables (metrics)
opinion and historical data play an and this reference condition is
especially important role in subsequently used to judge the
characterizing the reference condition biological status of other sites. There is
for these systems, as does the no independent (nonbiological)
application of innovative management definition of reference condition.
practices to obtain resource Reference condition and biological
improvement. responses are confirmed by identifying
severely impaired sites and then
In defining the biocriteria, managers comparing them with the derived
must strike a balance between the ideal reference condition to determine the
restoration of the water resource and the response(s) of biological indicators to
fact that human activity affects the impacts, and by selecting metrics that
environment. The most appropriate are known to respond to perturbation
course of action will be to use from other studies.
minimally impaired sites as
representing the maximum amount of A representative sample is taken of the
degradation that will be tolerated, entire population of estuary or coastal
thereby ensuring adherence to the marine sites (Figure 4-8). Sites that are
antidegradation policy of the CWA. known to be severely impaired may be

Figure 4-7
Hypothetical

cumulative
frequency
&XPXODWLYH )UHTXHQF\ SHUFHQW

distribution of
metric values for
all sites in a given
estuarine or
coastal marine
class. The dotted
line shows the
metric value
corresponding to
the 95th
percentile.

0LQLPXP 0D[LPXP
0HWULF 9DOXH
excluded from the sample, if desired. in running water or control-impact
The population distribution of each designs. It consists of selecting a
biological metric (Chapter 11) is reference site paired with each site to be
determined, and the 95th percentile of assessed. There is no characterization of
each metric is taken as its reference reference conditions for a physical class
value. The range from the minimum of estuarine or coastal marine waters;
possible value to the reference value is each test site and each reference site is a
trisected, and values in the top third of special case with each test site compared
the trisected range are presumed to be
to its reference site. Reference sites are
similar to reference conditions. Scoring
selected to be similar to their respective
of metrics is explained more fully in
test site, but unimpaired by the
Chapter 11.
perturbations of interest at the test site.
This approach may be less costly at the
outset because the design and logistics
A central assumption of the population
are simpler than the other approaches.
distribution approach is that at least
However, after several years of
some sites in the population of sites are
sampling and monitoring, costs for this
in good condition, which will be
approach are likely to be similar or
reflected in the highest scores of the
greater because each new test site
individual metrics. Because there is no
requires its own paired reference site.
independent definition of reference; i.e.,
independent of biological status,
The site-specific approach has two
reference conditions defined in this way
problems stemming from the fact that
must be taken as interim and subject to
there is usually only a single reference
future reinterpretation. Again,
site or a single nearby reference area
antidegradation safeguards must be in
from which reference sites are selected.
place to prevent further deterioration of
The first problem is representativeness:
the reference condition and criteria.
Does the reference site represent
reference conditions? Although the
4.4.3 Site-specific Reference Sites
reference site may lack the specific
stressor that is present at the test site,
The site-specific approach is analogous
unless carefully evaluated and placed, it
to upstream-downstream comparisons
Figure 4-8 Dry Season/Low Flow
Estuarine and coastal marine

biocriteria survey method useful
for stratified random (population Oligohaline
distribution) reference site
selection. Dry season/low flow
salinity pattern showing
mainstem sampling sites for
four salinity and three substrate
classifications.
Mesohaline
Polyhaline
Key
mud
transitional
sand
Marine
coastal land area
survey site
may be subject to other stressors that differences between a single test site and
have not been considered. its reference site may be due to
The second problem with the site- differences in impacts can not depend
specific approach is the potential for on statistical tests, but requires a careful
trivial statistical comparison of two sites weight-of-evidence evaluation (e.g.,
in that it is almost always possible to Hurlbert 1984, Schindler 1971).
demonstrate a statistically significant
difference between two sites by If the objective of a study is to test the
pseudoreplication (Hurlbert 1984). response of a particular metric, and if
Pseudoreplication is the repeated there are several paired sites, then a
measurement of a single experimental paired approach can be very powerful,
unit or sampling unit, and treating the allowing paired statistical tests (e.g.,
measurements as if they were Frydenborg 1994). A paired
independent replicates of the sampling experimental design is not
unit. A single reference site does not pseudoreplication because each site pair
yield sufficient information to is an independent replicate, and the
meaningfully judge the biological sample size (n) is the number of pairs.
relevance of a statistical difference at the
test site. The judgment that biotic

Example 1: Navigation channels - should be laid parallel to shore along
equal depth contours, with sampling
Navigation channels can represent an stations placed approximately evenly
important component of overall along the transect (Figure 4-10). For
estuarine areas (e.g., Houston Ship habitat consistency, the survey team
Channel, entrance to Chesapeake Bay should strive to maintain uniform depth,
and major harbors). Resource agencies bottom type, salinity, DO, and pH
may need to determine the relative characteristics at a minimum for all sites.
quality of navigation channels in
relation to the entire estuarine system as These parallel transects can evolve to an
part of the overall resource evaluation. open grid station array if sampling
stations are added around outfalls. In
Stations should be arrayed essentially in Figure 4-10, the D1-D5 series of stations
a nearfield-farfield pattern as shown in is added to the transect to reveal effluent
Figure 4-9, with farfield stations located distribution shifts around the discharge
"up" current and nearfield stations site. This approach addresses two
"down" current, outside the zone of aspects of effluent impact monitoring:
suspected impact. Stations should be (1) the relative biological community
located such that depth, grain size, and change near the discharge as compared
salinity remain consistent. These to the reference condition described by
conditions may be difficult to locate in a observation of either end of the transect;
tidally-influenced channel. and (2) the potential shifting, seasonal
Furthermore, if the navigation channel change, or expansion or contraction of
to be assessed is dredged to constant the zone of effluent influence from the
depth, changes in biota will primarily be discharge. Both forms of information are
a function of salinity, given uniform important to adequately assess the
poor substrate and the periodic biological effects of such effluents. This
destruction of the benthic habitat by design was used for bioassessment of
dredging. ocean outfalls from Delaware and
Maryland (see Chapter 13).
The reference condition for navigation
channels would be determined from the A complete grid, while more involved
central tendency (e.g., median) of the and expensive, would allow a more
biological data collected at "upstream" precise evaluation of the effects of these
stations, that is, those stations that are discharge plumes as they shift in
expected to be out of the zone of position in response to changes in
influence of impact sources (e.g., nearshore currents and seasonal shifts in
harbors, industrial areas). Sites from wave regime (Figure 4-10).
which the reference condition is
determined should be of comparable
depth, grain size, and salinity to those in
suspected impact zones and have the
same dredging history.
Example 2: Nearshore marine -
The station array in coastal marine

waters is essentially a variation of the
nearfield-farfield approach because of
the open water characteristics. Transects
Figure 4-9
Estuarine and
coastal marine
survey method for
navigation channel "Up" channel
assessment. stations
H a rbor Net
C u rre n t
Impact D ire c t i o n
Zone
"Down" channel
Key
Te s t s i t e s
stations
R e ference sites
Figure 4-10
n e t l o n g s h o r e c u rre n t
Estuarine and
coastal marine A
biocriteria survey B
method useful for C
D1 D3
marine site discharge D D4
selection. D2
E
D5
F
G

Chapter 5
Sampling Program Issues
Biological Assemblages
and Design
This chapter presents sampling program bioassessment. Each tier is comprised of

issues that are common to each of the a subset of assemblages, with the
three assessment tiers that employ field number of assemblages increasing in the
sampling. These issues include the higher tiers. While these six
biological assemblages (Section 5.1) that assemblages are described, specific
might be sampled, sampling design environmental circumstances and
strategies (Section 5.2 and 5.3), and budget constraints will determine what
logistical considerations (Section 5.4). subset each state uses. For example, if
Historically, benthic macroinvertebrates finances are extremely limited on the
have been the most widely sampled East Coast the single most effective
assemblage, which is described in detail assemblage to sample may be
in this chapter. macrophytes. On the West Coast
benthic macroinvertebrates or fish may
As described earlier in this document, a the assemblages of choice. The
possible sampling methodology is a bioassessment measurements are made
progressive tiered design, ranging from along transects extending from shore to
simple biological assessment to detailed, the deepest (channel) portion of the
intensive studies. The tiers are intended estuary, in a systematic grid along
to be implemented cumulatively, that is transects extending away from point
when possible, each tier should source discharges (nearfield/farfield), or
incorporate the elements in the in a probablistic design. The number of
preceding tier as appropriate for the transects or grid points, the assemblages
estuaries or coastal marine water in sampled, and the intensity of sampling
which they are applied. In general, the effort are determined by the assessment
methods are derived from those used tier with overall effort increasing at each
along the coastal United States (Dauer higher tier.
1993, Farrell 1993a, b, Nelson et al. 1993,
Word 1980, 1978, Word et al. 1976); in 5.1 Assemblages
Puget Sound (Eaton and Dinnel 1993); in
the EMAP - Estuaries program (Holland The study of any group of organisms
1990), and in USEPA’s National Estuary will yield information on the status of
Program (NEP) (USEPA 1992) and 403 their environment. The objectives in
Monitoring Program (USEPA 1994a). selecting assemblages for estuarine and
coastal marine bioassessment were to
Assessment tiers 1 through 3 require identify those that: (1) are
sampling biological assemblages and unambiguously useful for biological
habitats in one or more field visits. Six assessment; (2) can be sampled and
biological assemblages, including two interpreted in a cost-effective way; and
developmental/experimental (3) have easily calculated metrics that
assemblages, are recommended for can be used alone or in a multimetric
estuarine and coastal marine waters index of the assemblage. Assemblages
that meet these criteria are suggested for habitat qualities (Holland 1990, Plafkin
use in estuarine and coastal marine et al. 1989), are not very mobile, and
assessment; assemblages that do not consequently, integrate long-term
presently meet the criteria are changes in these ecosystem components.
considered to be developmental. For those reasons, benthic
Suggested assemblages include infaunal macroinvertebrates tend to dominate
benthic macroinvertebrates, fish, aquatic this text.
macrophytes, and phytoplankton
(chlorophyll a). The developmental Individual macroinvertebrate species
assemblages include zooplankton, have sensitive life stages that respond to
epibenthos, and paleoenvironmental stress and integrate effects of short-term
systems. These developmental environmental variations, whereas
assemblages are promising, but they community composition depends on
lack the same level of refinement long-term environmental conditions. In
documented for the suggested addition to taxonomic identification,
assemblages listed above and benthic macroinvertebrate metrics may
unresolved technical problems remain require knowledge of the feeding group
with respect to cost-effective assessment to which a species belongs, for example,
and interpretation. Background and suspension feeders and deposit feeders.
rationale for these suggested Potential metrics for estuarine and
assemblages was presented in Chapter 2. coastal marine benthos are listed in
Table 5-1. Metrics considered in the
Multimetric bioassessment is not a EMAP Estuaries program are listed in
ready-made, one-size-fits-all instrument Table 5-2.
that will tell managers whether estuaries
or coastal marine waters are healthy. It Sampling Strategies
is an approach that is expected to be
modified to specific regional conditions The sampling area should focus on the
before it can be applied. For example, most predominant substrate available
bioassessment of streams has been (in many estuaries and coastal marine
successful when modified and calibrated areas this will be soft sediments of mud
regionally (e.g., Barbour et al. 1996a, through sand grain sizes), and the
Ohio EPA 1990, Miller et al. 1988), but it metrics should be developed
has been less successful when used "off- independent of microhabitat variation
the-shelf." Successful application (Table 5-3). The type of sampling gear
requires region-specific selection and will depend on the substrate being
calibration of metrics, as well as regional sampled; each substrate has its own
characterization of reference conditions. optimal sampling gear (Section 5.1.1.4).
For example, benthic infauna are rare in Standardized sampling techniques for
rocky, fjord-type estuaries and would be each gear type should be followed to
an inappropriate assemblage to sample allow for the comparison of data.
in such a setting. Processing of samples should be
standardized by using a mesh size
5.1.1 Benthic Macroinvertebrates appropriate to the region. In the past,
(Infauna) monitoring programs conducted in east
coast waters have often used a 0.5-mm
Benthic macroinvertebrates are an mesh screen, while west coast programs
appropriate assemblage for all biological have used a 1.0-mm screen (Bowman et
assessments of water bodies because al. 1993). States should consider testing
they respond to water, sediment, and various mesh size screens to determine
5-2 Sampling Program Issues

Table 5-1. Potential benthic macroinvertebrate metrics.
M etric Response to Impairment
No. of taxa reduced
Mean no. of individuals per taxon substantially lower or higher
% contribution of dominant taxon elevated
Shan non-W iener diversity reduced
Total biomass substantially lower or higher
% biomass of opportunistic species elevated
% abundance of opportunistic species elevated
Equilibrium species biomass reduced
Equilibrium species abundance reduced
% taxa below 5-cm reduced
% biomass below 5-cm reduced
% carnivores and omnivores elevated
No. of amphipod species reduced
% individuals as amphipods reduced
% individuals as polychaetes/oligochaetes elevated
No. of bivalve species reduced
% individuals as molluscs reduced
% individuals as depos it feeders elevated
Mean size of organism in habitat reduced
Proportion of expe cte d no. o f sp ecies in sa m ple reduced
Propo rtion of expected no. of spec ies at site reduced
Mea n weight pe r individual polychaete reduced
No. of sus pension fe eders reduced
% individuals as suspen sion feede rs reduced
No. of gastropod species reduced
No. of Capitellid polychaete species elevated
the most appropriate size for their Time and Costs

bioassessment activities. Ferraro et al.
(1994) present a process to evaluate the An informal survey of some states that
optimum infaunal sampling protocol; conduct routine monitoring of estuaries
i.e., sampling unit area, sieve mesh size, and coastal marine waters indicates that
and sample size [n], discussed more estuarine sampling requires a minimum
fully in Section 5.2.6. of two full-time equivalent (FTE) staff,
Table 5-2. Metrics from which the EMAP Virginian and Louisianian benthic indexes were
developed. Louisianian Province has reduced number of metrics due to
knowledge gained from previous Virginian province studies (n.a. - not applicable).
Community Metrics
Measure of
Structure/
Function
Virginian Province
Biodiversity/ Proportion of expected number of species present in a sample # Proportion of expected

Species number of species present at a site # Shannon-W einer Diversity Index # Pielou’s evenness
Richness index
Abundance Total benthic abundance per event # Mean benthic abundance per sample # Total benthic
Measures biomass per event # Mean benthic biomass per sample
Individual Health Biomass/abundance ratio # Mean weight per individual polychaete # Mean weight per
individual mollusc
Functional Number of suspension feeding organisms per event # Biomass of suspension feeding
Groups organisms per event # Percent of total benthic abundance as suspension feeders # Percent
of total benthic abundance as suspension feeding biomass # Number of deposit feeding
organisms per event # Biomass of deposit feeding organisms per event # Percent of total
benthic abundance as deposit feeding organisms # Number of benthic omnivores/predators
per event # Biomass of benthic omnivores/predators per event # Percent of total benthic
abundance as omnivores/predators # Percent of total benthic biomass as
omnivores/predators # Number of opportunistic species per event # Mean number of
opportunistic species per sample # Percent of total benthic abundance as opportunists #
Number of equilibrium species per event # Mean number of equilibrium species per sample #
Percent of total benthic abundance as equilibrium species # Percent of mean benthic
abundance as equilibrium species
Taxonomic Number of amphipods per event # Amphipod biomass per event # Percent of total benthic
Composition abundance as amphipods # Percent of total benthic biomass as amphipods # Number of
bivalves per event # Bivalve biomass per event # Percent of total benthic abundance as
bivalves # Percent of total benthic biomass as bivalves # Number of gastropods per event #
Gastropod biomass per event # Percent of total benthic abundance as gastropods # Percent
of total benthic biomass as gastropods # Number of molluscs per event # Mollusc biomass
per event # Percent of total benthic abundance as molluscs # Percent of total benthic
biomass as molluscs # Number of polychaetes per event # Polychaete biomass per event #
Percent of total benthic abundance as polychaetes # Percent of total benthic biomass as
polychaetes # Number of Capitellid polychaetes per event # Percent of total benthic
abundance as Capitellid polychaetes # Number of Spionid polychaetes per event # Percent
of total benthic abundance as Spionid polychaetes # Percent of total polychaete abundance
as Spionid polychaetes # Number of Tubificid oligochaetes per event # Percent of total
benthic abundance as Tubificid oligochaetes
Louisianian Province
Biodiversity/ Shannon-W iener Diversity Index # Pielou’s Evenness Index # Mean number of species #
Species Mean number of polychaete species
Richness
Abundance Mean benthic abundance per site

Measures
Individual Health n.a.
Taxonomic Mean abundance of amphipods per site # Proportion of total benthic abundance as
Composition amphipods # Mean abundance of decapods per site # Proportion of total benthic abundance
as decapods # Mean abundance of bivalves per site # Proportion of total benthic abundance
as bivalves # Mean abundance of gastropods per site # Proportion of total benthic
abundance as gastropods # Mean abundance of molluscs per site # Proportion of total
benthic abundance as molluscs # Mean abundance of polychaetes per site # Proportion of
total benthic abundance as polychaetes # Mean abundance of Capitellid polychaetes per site
# Proportion of total benthic abundance as Capitellid polychaetes # Mean abundance of
Spionid polychaetes per site # Proportion of total benthic abundance as Spionid polychaetes
# Proportion of total polychaete abundance as Spionid polychaetes # Mean abundance of
Tubificid oligochaetes per site # Proportion of total benthic abundance as Tubificid
oligochaetes

Table 5-3. Sampling summary for infaunal benthic macroinvertebrates.
Habitat Preferred: soft sedim ents (m ud-sand ).
Sampling Regiona lly mos t appropriate for substrate (Tab le 5-4).

Gear
Index Re gionally most appro priate

Period Preferred:
Sum mer - East & Gulf Coast
Spring - Pacific Northwest
Alternative:
All four seasons, or winter and summ er
Sampling Preferred: samples from 3 grabs at each of at least 10 sites.

Alternative: keep sites as replicates if a within-class variance
estim ate w ill be use d in as ses sm ent.
Analysis Preferred: lowe st p ractic al taxonom ic level

Alte rnative: identificatio n to class and fa m ily.
and has an associated per sample cost of stations and parameters as indicated by
$200 - $400. the data.
Coastal marine sampling requires a Gear Type

minimum of four FTEs, and has an
associated cost of $400 - $800. Three All sampling methods and gear types
months to a year are required from time have specific biases because they capture
of sampling to preparation of an a target assemblage. Because estuaries
interpretive report. and coastal marine waters are complex
environments with a potentially large
Assessment Tiers number of habitats, it is important to
choose sampling methods and gear
The benthic infaunal assemblage is appropriate for a specific habitat type.
appropriate for all three field tiers Sampling within a given habitat type
outlined for the biological assessment of such as a salinity regime, bottom grain
estuaries and coastal marine waters. size, and/or depth should be conducted
Tier 1 determines the presence/absence so that samples can be considered
of macroinvertebrates below 5-cm depth representative of the community being
in the sediment and briefly describes the studied.
class and family of observed benthos.
Tier 2 determines the major taxa and A large number of benthic sampling
indicator species present in each sample methods and gear are available. The
to the genus and species level. Tier 3 choice of appropriate methods and gear
applies a full benthic community will depend upon the goals of the
assessment, recording the numbers of sampling and the habitat to be sampled.
individuals in each grab to the genus
and species level, and can include < In subtidal areas, benthic infauna
determination of biomass if deemed can be collected using grabs, such as
appropriate by the state. Tier 3 uses the Young, Ponar, or Van Veen; or cores
benthic community assessment with such as box, gravity, or hand-held
replication and additional diagnostic cores collected by divers. Grab or
core size and number of replicates < Allows vertical sectioning of
should be sufficient to adequately undisturbed samples for profile
sample the infaunal community, examination.
bearing in mind that distribution is
usually spatially clumped rather Penetration well below the desired
than random or regular; and sampling depth is preferred to prevent
sample disturbance as the device closes.
< Intertidal areas may best be sampled It is best to use a sampler that has a
at low tide with hand-held cores. means of weight adjustment so that
For certain infauna it may also be penetration depths may be modified
feasible to estimate abundance by with changing sediment type (USEPA
counting the number of surface 1992).
structures within a given area. For
example, some polychaete worms Grab Samplers
build identifiable tube or mound
structures, or leave identifiable fecal Well designed and constructed grab
coils in intertidal areas. If the local samplers are capable of consistently
infauna has been studied to the sampling bottom habitats. Depending
extent that identification of such on the size of the device, areas of 0.02- to
topographic features can be 0.5-m2 and depths ranging from 5- to 15-
correlated to the presence of a cm may be sampled. Limitations of grab
particular organism, crude samplers include:
abundance and presence/absence
evaluations may be possible. < Variability among samples in
penetration depth depending on
Collection of sediments and benthic sediment properties;
organisms should be done concurrently
in order to reduce the costs of field < Oblique angles of penetration which
sampling and to permit sound result in varying penetration depths
correlation and multivariate analyses. within a sample; and
Therefore, the sampling equipment and
procedure should also include sampling < The sample may be folded or
the sediment. otherwise distributed by some
devices, such as the Shipek sampler,
Desirable attributes for sediment resulting in the loss of information
sampling gear include: concerning the vertical structure of
benthic communities in the
< Creates a minimal pressure wave sediments.
when descending;
However, careful use of these devices
< Forms a nearly leakproof seal when will provide reliable quantitative data.
the sediment sample is taken; Grab samplers are the tools of choice for
a number of estuarine and marine
< Prevents winnowing and excessive monitoring programs due to their ability
sample disturbance when ascending; to provide quantitative data at a
relatively low cost (Fredette et al. 1989,
< Allows easy access to the sample USEPA 1986-1991). Various grab
surface so that undisturbed samplers which could be used for Tiers
subsamples may be taken; 1-3 are summarized in Table 5-4.

Table 5-4. Summary of bottom sampling equipment (Ad apted from US EP A 1992, K lem m et al.
1992, and A STM 1998b).
.
DEVICE USE ADVANTAGES DISADVANTAGES
Soft sediments Samples a variety of soft substrates Samples limited surface area.
KB Corer
only. up to harder types. Sampling 2tube Requires boat and winch.
can be modified up to 100-cm
substrate surface; least disturbance
to water/bottom interface. Can be
used in shallow to medium-shallow
water up to 30.5-m or deeper.
Soft sediment Good penetration on soft sediment. Heavy; requires boat and winch.
Ballcheck Single and
only. Small sample volume allows greater Does not retain sand unless
number of replicates to be collected bronze core retainers are used.
in a short time period. Samples deep
Multiple Tube
burrowing organisms. Used in

shallow to deep water (3-m to 183-m).
Automatic check valves prevent
sample loss.
Shallow wadeable Preserves layering and permits Small sample size requires
Fluorocarbon plastic
waters or deep historical study of sediment repetitive sampling. Impractical

waters if SCUBA deposition. Rapid-samples in water > 1-m depth if SCUBA
available. Soft or immediately ready for laboratory not available.
semi-consolidated shipment. Minimal risk of
or Glass Tube
deposits contamination.
Same as above Handles provide for greater ease of Careful handling necessary to
removable Fluorocarbon
except more substrate penetration. Above prevent spillage. Requires

plastic or glass liners.
consolidated advantages. removal of liners before

sediments can be repetitive sampling. Slight risk
obtained. of metal contamination from
Hand Corer with
barrel and core cutter.

Corer
Same as above. Collection of large undisturbed Hard to handle.

Box
sample allowing for subsampling.

Phleger (Gravity)
Semi-consolidated Low risk of sample contamination. Careful handling necessary to

sediments. Maintains sediment integrity relatively avoid sediment spillage. Small
well. sample, requires repetitive
operation and removal of liners.
Time consuming.
Corer
Lakes, estuarine Eliminates metal contamination if Expensive, heavy, requires boat

Young Grab
and marine areas. grab is plastic or kynar lined. and winch.

Reduced pressure wave. Can
subsample. Better penetration in
sand than the modified Van Veen.
Soft to semi-soft Obtains a larger sample than coring Possible incomplete jaw closure
Ekman or Box
sediments. Can tubes. Can be subsampled through and sample loss. Possible
be used from boat, box lid. Hinged top doors reduce shock wave which may disturb
bridge, or pier in washout, shock waves and substrate the fines. Metal construction
waters of various disturbance. Range of sizes may introduce contaminants.
Dredge
depths. Weights available. Possible loss of fines on

can be added for retrieval. Inefficient in deep
deeper penetration water or where even moderate
in fine sand. current exists.
Table 5-4 (Cont’d). Summary of bottom sampling equipment (Adapted from USE PA 1992,
Klem m et al. 1992, and A STM 1998b).
DEVICE USE ADVANTAGES DISADVANTAGES

Useful on sand, Most universal grab sampler. Shock wave from descent may
Ponar Grab Sampler
silt, or clay. Adequate on most substrates; very disturb fines. Possible
efficient for hard sediments. Large incomplete closure of jaws
sample obtained intact permitting results in sample loss. Possible
subsampling. Better penetration than contamination from metal frame
other grabs; sideplates and screens construction. Sample must be
reduce washout, shock waves and further prepared for analysis. A
substrate disturbance. very heavy grab requires use of
a boat with winch and cable.
Shell hash can hold jaws open
causing loss of sample. Must
use stainless-lined grab for
sediment metals samples.
Waters of 1-2-m Piston provides for greater sample Cores must be extruded on site
BMH-53 Piston
deep when used retention. to other containers - metal

with extension rod. barrels introduce risk of metal
Soft to semi- contamination.
consolidated
deposits.
Cover
BMH-60 Modified Van Veen
Useful on sand, Adequate on most substrates. Large Requires boat and winch.
silt, or clay. sample obtained intact. Shock wave from descent may
disturb fines. Possible
incomplete closure of jaws
results in sample loss. Possible
contamination from metal frame
construction. Sample must be
further prepared for analysis.
Limited penetration in hard
sand. Possible overpenetration
in soft silt.
Sampling moving Streamlined configuration allows Possible contamination from
waters from a fixed sampling where other devices could metal construction.
platform. not achieve proper orientation. Subsampling difficult. Not
effective for sampling fine
sediments.
Smith-McIntyre
Useful on most Reduced pressure wave. Designed Loss of fines. Heavy; requires
substrates. for sampling hard substrates. Can boat and winch. Possible metal
subsample and make vertical cross- contamination unless grab is
sections. Greater penetration in sand lined.
and cobble than modified Van Veen,
but possibly not as deep as a Young
Grab
grab. Better closure in areas with

wood debris.
Useful on most Inexpensive, easy to handle. Loss of fines on retrieval

Scoops, Drag
substrates. through water column. Layer

Various information not collected.
environments
Buckets
depending on
depth and
substrate.
The number and kinds of (Klemm et al. 1992). USEPA EMAP-

macroinvertebrates collected by a Estuaries protocols describe a simple
particular grab may be affected by the and consistent method for accepting or
habitat sampled, substrate type rejecting a bottom grab (Figure 5-1).
sampled, depth of penetration, angle of
closure, completeness of closure of the The type and size of the grab samples
jaws and potential loss of sample (or other device) selected for use will
material during retrieval, creation of a depend on factors such as the size of
"shock" wave and "washout" of boat, available winch and hoisting gear,
organisms at the surface of the substrate. the type of sediment to be sampled,
The high-flow velocities often water depth, current velocity, and
encountered in rivers and wave action in whether sampling is conducted in
estuaries and coastal marine waters can sheltered areas or open water (Klemm et
also affect stability of the sampler al. 1992). The EMAP-Near Coastal

Figure 5-1
Cross-section of
sediment in
clamshell bucket
illustrating
acceptable and
unacceptable
grabs.
Acceptable if Minimum
Unacceptable
Penetration Requirement Met
(Washed, Rock Caught in Jaws)
and Overlying Water is Present
Unacceptable (Canted with Unacceptable

Partial Sample) (Washed)
Program selected a Young grab into the sediment. The standard Ponar
(sometimes referred to as a Young- takes a sample area of 523-cm2. A small
modified Van Veen) that samples a version, the petite Ponar grab, takes a
surface area of 440-cm2 (Weisberg et al. sample area of 232-cm2 and can be used
1993). This Young grab was selected in habitats where there may be an
because it deploys easily from small unusual abundance of
boats (24-ft) and it samples sand and macroinvertebrates, thus eliminating the
mud habitats adequately. The need to subsample.
maximum penetration depth of the grab
was 10-cm. The weight of the standard Ponar grab
makes it necessary to use a winch and
PONAR Grab: cable or portable crane for retrieving the
sample, and ideally the samples should
The PONAR has side plates and a screen be taken from a stationary boat. The
on the top of the sample compartment to smaller version (petite Ponar grab) is
prevent loss of the sample during designed for hand-line operation, but it
closure. With one set of weights, this may be used with a winch and cable.
heavy steel sampler can weigh 20-kg.
Word et al. (1976) report that the large Ekman Grab:
amount of surface disturbance
associated with Ponar grabs can be The Ekman grab sampler is used to
greatly reduced by simply installing obtain samples of macroinvertebrates
hinges rather than fixed screen tops, from soft sediments, such as very fine
which will reduce the pressure wave sand, mud, silt, and sludge where there
associated with the sampler's descent is little current. This grab is inefficient
in deep waters, under adverse weather touches the bottom. The jaws close
conditions, and in waters with moderate when positioned properly on the
to strong currents or wave action. The bottom, and retain a discrete sample of
Wildco box corer is like a heavy duty sediment to be brought to the surface for
Ekman with a frame and weights and processing. The device is heavy and can
can be used to collect macroinverte- weigh 45.4-kg or more. The chief
brates in estuaries. Because of its weight advantage of the sampler is its stability
a winch is necessary for retrieving the and easier control in deep and rough
sample from a stationary boat. waters. The spring-loaded jaws of the
Smith-McIntyre grab must be considered
The Ekman grab sampler is a box- a hazard and caution should be
shaped device with two scoop-like jaws exercised when using the device. Due to
that must penetrate the intended the weight and size, this device must be
substrate without disturbing the water- used from a vessel with boom and lifting
sediment boundary layer, close when capabilities.
positioned properly on the bottom, and
retain a discrete sample of sediment Modified Van Veen Grab:
while it is brought to the surface for
processing. Hinged doors on the top of The modified Van Veen grab sampler is
the grab prevent washout during sample used to obtain samples of
retrieval. The grab is made of 12- to 20- macroinvertebrates from sediments in
gauge brass or stainless steel and weighs estuaries and other marine habitats.
approximately 32-kg. The box-like part This device is useful for sampling sand,
holding the sample has spring-operated gravel, mud, clay and similar substrates
jaws on the bottom that must be and is available in three sizes: 0.06-m2 ,
manually set. The sampler is available 0.1-m2 , and 0.2-m2 . Larger versions of
in several sizes; however, in very soft this grab are available, and their use is
substrates only a tall model should be dependent upon the type of bottom to be
used, either a 23-cm or a 30.5-cm model. sampled, and the type of vessel available
The Ekman grab can be operated from a to deploy the sampler.
boat with a winch and cable.
The modified Van Veen grab sampler
Smith-McIntyre Grab: has paired jaws that penetrate the
intended substrate without disturbing
The Smith-McIntyre grab sampler is the water-sediment boundary layer.
designed to obtain samples of They are closed by the pincher-like
macroinvertebrates from sediments in action of two long arms. The long arms
rough weather and deep water in give added leverage for penetrating
estuaries and oceans. This device hard sediments.
samples a surface area of 0.1-m2 and is
useful for sampling macroinvertebrates The modified Van Veen is basically an
from a broad array of sand, gravel, mud, improved version of the Petersen grab in
clay, and similar substrates. that long arms have been attached to the
jaws to help stabilize the grab on the
The Smith-McIntyre grab sampler has bottom in the open sea just prior to or
hinged top doors to prevent sample during closure of the device. This grab
washout and the pressure wave in is used extensively in Puget Sound for
descent. Its paired jaws are forced into the ambient monitoring program and for
the intended substrate by two "loaded" pollution-related surveys. Large hinged
strong coiled springs when the grab screen doors with rubber flaps have

been added to the top of the sampler for McIntyre provides better access to the
access to the surface of the sample. sample while the Young grab is easier
Additional weights can be applied to the and safer to operate, especially in rough
modified Van Veen jaws to effect greater weather. An advantage of both designs
penetration in sediments, although is that the retrieved sample can be cross-
penetration is not as deep in hard sand sectioned and examined intact, although
or cobble as with the Young grab or the this is easier with the Smith-McIntyre
Smith-McIntyre. design.
Young Grab: Core Samplers
The Young grab sampler is similar in Core samplers use a surrounding frame
operation to the Van Veen and the to ensure vertical entry; vertical
Smith-McIntyre, but the sample can be sectioning of the sample is possible
accessed undisturbed from the top of the (USEPA 1986-1991). Coring devices can
grab through hinged doors like a Smith- be used at various depths in any
McIntyre. It is encircled by a ring-like substrate that is sufficiently compacted
frame which enhances flat, stable so that an undisturbed sample is
landings of the grab on the substrate. retained; however, they are best suited
Weights can be added to the frame to for sampling the relatively homogenous
aid penetration in hard sand or cobble. soft sediments, such as clay, silt, or sand
A major advantage of the Young grab is of the deeper portions of estuaries and
efficient performance without the risk of coastal marine waters. Because of the
injury associated with the spring-loaded small area sampled, data from coring
Smith-McIntyre. This grab can be devices are likely to provide very
provided in a 0.044-m2 and a 0.1-m2 imprecise estimates of the standing crop
version. The former is appropriate to of macrobenthos.
small boat operations while the latter
size is more effective for marine work KB, Ballcheck, and Phleger Corers:
and obviously requires fewer lowerings
or "drops" to obtain the same volume of KB type, Ballcheck, and Phleger corers
material and community representation. are examples of devices used in shallow
or deep water; they depend on gravity to
Recent comparisons of the Young and drive them into the sediment. The cores
Smith-McIntyre grabs in rough Atlantic are designed so that they retain the
waters revealed consistently greater sample as it is withdrawn from the
volumes of sediment collected by the sediment and returned to the surface.
Young grab in six trials each in soft Hand corers designed for manual
sandy muds, sand, packed sand, and operation are used in shallow water.
sand and gravel sediments. While the Sections of the core can be extruded and
grabs were the same size (0.1-m2 ) and preserved separately or the entire core
had the same weight attached, the can be retained in the tube and
significant factor in performance was the processed in the field or laboratory.
design differences of the two grabs Intact cores can also be preserved by
(Gibson 1995, unpublished). freezing and processed later.
While either the 0.1-m2 Young or Smith- Additional replication with corers is
McIntyre designs are effective off-shore feasible because of the small amount of
grabs for the biocriteria development material per sample that must be
purposes of this guidance, the Smith- handled in the laboratory. Multiple-
head corers have been used in an they are appropriate for quantitative
attempt to reduce the field sampling sampling in all shallow-water benthic
effort that must be expended to collect habitats and can be deployed from small
large series of core samples (Flannagan boats. They probably represent the only
1970). quantitative device suitable for sampling
shallow-water habitats containing
The Dendy inverting sampler (Welch stands of rooted vascular plants and
1948) is a highly efficient coring-type they will collect organisms inhabiting
device used for sampling at depths to 2- the vegetative substrates as well as those
or 3-m in nonvegetated substrates living in sediments.
ranging from soft mud through coarse
sand. Because of the small surface area In marine waters, benthic macrofauna
sampled, data obtained by this sampler are generally collected using various box
suffer from the same lack of precision cores deployed from ships or other
(Kajak 1963) as the coring devices platforms, or diver operated cores. A
described above. Since the per-sample box coring device consisting of a
processing time is reduced, as with the rectangular corer having a cutting arm
corers, large numbers of replicates can which can seal the sample prior to
be collected. retraction from the bottom should be
used. In order to sample a sufficient
Stovepipe-type devices include the number of individuals and species, and
Wilding sampler (Wilding 1940, APHA to integrate the patchy distribution of
1992) and any tubular material such as fauna, each sample should have a
60- to 75-cm sections of standard 17-cm surface area of no less than 100-cm2 and
diameter stovepipe (Kajak 1963) or 75- a sediment depth of at least 20-cm. In
cm sections of 30-cm diameter sediments having deep, burrowing
aluminum irrigation pipe fitted with fauna, a box corer capable of sampling
handles. In use, the irrigation pipe or deeper sediment may be needed. In
commercial stovepipe is manually sandier sediments, it may be necessary
forced into the substrate, after which the to substitute a grab sampler for the box
contained vegetation and coarse corer in order to achieve adequate
substrate materials are removed by sediment penetration. Visual inspection
hand. The remaining materials are of each sample is necessary to insure
repeatedly stirred into suspension, that an undisturbed and adequate
removed with a long-handled dipper amount of sample is collected.
and poured through a wooden-framed
floating sieve. Because of the laborious Sieve Mesh Size
and repetitive process of stirring,
dipping, and sieving large volumes of The use of different sieve mesh sizes for
material, the collection of a sample often screening benthic samples limits the
requires 20- to 30-minutes. comparability of results between marine
monitoring studies (Reish 1959; Rees
The use of stovepipe samplers is limited 1984). The major advantage of using a
to standing or slowly moving waters smaller mesh size is the retention of both
having a maximum depth of less than juvenile and adult organisms as well as
60-cm. Since problems relating to depth large-and small-bodied taxa. The major
of sediment penetration, changes in disadvantage is the concomitant
cross-sectional area with depth of increased cost of sample processing. For
penetration, and escape of organisms are example, using a 0.5-mm mesh rather
circumvented by stovepipe samplers, than a 1.0-mm mesh could increase

retention of total macrofaunal organisms subcores that should be taken will
by 130 to 180%; however, costs for depend upon the variability of the
processing the samples may increase as infaunal community. Representative
much as 200% (USEPA 1986-1991). subsampling can be difficult to
achieve if benthic species have
It is recommended that a standard mesh patchy or clumped distributions.
size be selected for all monitoring Subsampling can also damage
studies. A review of estuarine collected organisms (e.g., polychaete
monitoring programs from around the worms), decreasing the number of
country (Bowman et al. 1993) showed specimens that can be identified to
that both 0.5- and 1.0-mm mesh sizes are genus or species;
used, with a slight majority of the
programs reviewed using a 0.5-mm < Several studies have examined the
mesh screen (Table 5-5). Dauer (1993) effect of varying levels of taxonomic
evaluated biocriteria developed from analysis on the results of statistical
data collected as part of the Virginia measures of the infaunal community
Benthic Biological Monitoring Program (e.g., Ferraro and Cole 1990, 1992,
using a 0.5-mm mesh screen. 1995, Warwick 1988, Warwick et al.
1990). The studies indicate that in
Sieving can be done either aboard the some instances species-level
survey vessel or on shore after the taxonomic identification does not
cruise. Sieving occurs prior to fixation yield any more information than
(sample preservation) aboard the vessel, family- or even phylum-level
whereas waiting until after the cruise identification. The degree of
requires fixation prior to sieving. If taxonomic proficiency required to
inadequate concentrations of fixative are adequately characterize the
added and deterioration or community will depend upon the
decomposition of organisms occurs, diversity present in the community.
there may be significant sample Species level identification is
degradation. If large numbers of necessary and cost-effective for fish
samples are to be collected, field sieving surveys. However, while this is
reduces sample storage requirements as desired for macroinvertebrates, it is
well as the modification/loss of data often too costly and assessment
(USEPA 1992, 1994d). needs can usually be met at the
genus level.
After samples have been collected, the
samples must be processed so that data Although species-level identifications
can be collected and analyzed. Two may not be necessary for classifying sites
aspects of sample processing of as minimally impaired or impaired, this
particular concern are the subsampling degree of taxonomic identification may
and identification that may occur in the be required to assess the sources of
field or laboratory. Sorting procedures impairment using data collected in Tier
are described in Klemm et al. (1992). 3. Species-level identifications require
greater taxonomic expertise than do
< Subsampling of benthic infauna can higher taxonomic divisions; this species
be accomplished by subcoring; i.e., level of expertise may not be as readily
removing smaller core samples from available to state agencies. If this is the
within a grab or core sample, and case, then state resource managers must
sorting all organisms found within determine whether the cost of
the subcore. The size and number of
Table 5-5. Mesh sizes used in estuary benthic monitoring programs.
Mo nitoring Program Me sh Size (m m ) Reference
Chesapeake Bay 0.5 Dauer 1993, Holland et al.

198 7, 1988, 1989 ,
Ranasinghe et al. 1992
Tar/Pamlico 0.5 Eaton 199 2a-d
EMAP-Near Coastal 0.5 USEPA 1992, W eisberg et

al. 1993, Holland 1990
Naples Bay, Florida 0.595 Simpson et al. 1979
Puget Sound Ambient 1.0 PSW QA 1988, 1990, 1991

Monitoring Program
Puget So und Es tuary 1.0 Simenstad et al. 1991

Program
contracting these identifications is conditions in estuaries and coastal

justified based on the information marine waters; some fish species may
obtained and the assessment tier to also be influenced by management
which it would be applied. One (stocking), angling, and commercial
approach to this problem of obtaining harvesting; and unbiased sampling is
sufficient taxonomic expertise is for the difficult because each feasible gear type
states of a region to cooperate in a joint is highly selective.
venture to employ the taxonomic
expertise necessary to all. In this Sampling Gear
manner the cost of a skilled taxonomist,
either contracted or on staff, can be Fish communities may vary
shared. considerably among the numerous
habitat types that may be present in a
5.1.2 Fish target estuary or coastal marine area.
The choice of sampling method and gear
Fish communities include species in a type will depend upon the habitat and
variety of trophic levels (omnivores, the fish species of interest. Shallow
herbivores, planktivores, piscivores). areas may best be sampled using dip
Fish are long-lived, integrate long- and nets or beach seines, while deeper
short-term changes, and they also waters may be sampled using gill nets,
integrate effects of lower trophic levels; purse seines, or otter trawls. Net and
thus, fish community structure is a good mesh size should be appropriate to
measure of integrated environmental allow a representative sample of target
health. Estuarine and coastal marine fish to be obtained. Fishing effort
fish receive a large amount of public should be comparable among stations
attention because of sport and with constant tow distances, times,
commercial fishing and attendant speeds, and lengths of trawl warps.
concerns regarding fish production and Because there is no easy way of
safety for human consumption. On the estimating population size in any given
negative side, fish may be wide-ranging area of an estuary or coastal marine area,
or migratory and might not reflect local consistency in effort is of the utmost

importance to allow legitimate and Secchi depth are also taken in the
comparisons among sites. trawling area. Water quality is sampled
at surface, mid, and bottom depths.
Maryland DNR’s IBI sampling These measurements have proven useful
techniques are designed to sample the in relating water quality parameters to
nearshore fish communities in the tidal fish communities. A summary of fish
tributaries of the Chesapeake Bay. They sampling is given in Table 5-6.
were modeled after the Maryland
Striped Bass Juvenile Seine Survey < Subsampling of fish collected using
which has been ongoing since 1954 any of the sampling methods
(Goodyear 1985). Two beach seines are mentioned above is problematic. It
pulled at each site allowing a half hour is probably most efficient and
interval between hauls for repopulation statistically valid to identify and
of the seine area. Seines are pulled with make external measurements and
the tide employing a “quarter sweep” observations of all fish caught
method where one end of the seine is during a given tow or time period.
held on shore while the other end is
fully extended perpendicular to shore, < The level of taxonomic identification
and then pulled back into shore forming required to effectively characterize
a semi-circle. The seine used is a bagless the fish community will depend
6.4-mm mesh seine 30.5-m in length and upon the diversity of the community
1.2-m deep. Precautions are taken upon being sampled and the metrics being
approaching the site to avoid used to evaluate the data.
disturbance of the sampling area. Identification to species is preferable
for most individuals taken in a given
Concurrent trawls are pulled with the area. Individuals that cannot be
tide in the channel adjacent to shore. A field-identified should be preserved
small otter trawl (3.1-m with 12.8-mm and returned to the lab for
stretch mesh, and 50.8-cm x 25.4-cm identification.
doors) with tickler chains is used to
sample the bottom community local to 5.1.3 Aquatic Macrophytes
the seine sample area. Water quality
measurements (temperature, dissolved Macrophytes form an integral part of the
oxygen, pH, conductivity, and salinity) littoral zone of many estuaries and
Table 5-6. Sampling summary for fish.
Habitat Su blitto ral.
Sampling Gear Se ines and any gear that effective ly captu res bottom -feeding and pelagic
fish, usually otter trawls.
Index Period Any season can be selected depending upon migration and recruitment
patterns in the region. Seasonal sampling might be needed to assess
particular problems.
Sampling Bo ttom -feeding and pelagic fish. Su fficie nt s ets of gear to obtain
represe ntative species counts (us ually 4 or more ).
Analysis Collected species are weighed, measured, and examined for external
abnormalities (lesions, growths, deformities). Histopathology may be
performed.
coastal marine waters, serving as habitat human perspective, problems might
for fish and invertebrates as well as include loss of aesthetic appeal,
being a distinct biological assemblage. decreases in desirable commercial and
For many estuaries, the areal extent and game fishes, and loss of recreational
distribution of SAV is used as an access caused by increased macrophyte
indicator of estuarine quality (Batiuk et production.
al. 1992). Ecosystems whose primary
producer component is dominated by Phytoplankton standing stock is
aquatic macrophytes can be transformed measured by surface chlorophyll a
to macro algae or phytoplankton- concentration, sampled at the 0.5-m
dominated systems through nutrient depth at each sampling site (Table 5-9).
enrichment. Increased nutrient input Tiers 1 and 2 can use a single
stimulates macrophyte growth; measurement taken at each sampling
however, it also promotes growth of site with a fluorometer attached to a
periphyton and phytoplankton, which conductivity-temperature-depth meter
shade the SAV. The shading reduces (CTD) (USEPA 1994c) taken from June
macrophyte growth and survival through September. Alternatively,
(Dennison et al. 1993, Batiuk et al. 1992). chlorophyll a may be determined
Overall, macrophyte standing stock is an spectrophotometrically on
excellent indicator of estuarine water phytoplankton samples returned to the
quality. The presence of confounding lab. Tier 2 can include identification of
factors, such as diseases, can be dominant taxa, including nuisance taxa.
determined from examination of Tier 3 uses a seasonal or annual average
affected plants, or from historical surface chlorophyll concentration from
information. Potential macrophyte all stations over all sampling events and
metrics are listed in Table 5-7 and the can include full characterization of the
recommended sampling protocol for phytoplankton community.
macrophytes is summarized in Table 5-
8. Field sampling can be performed in a If phytoplankton communities are to be
single visit. Plants are identified and sampled, several techniques may be
weighed on-site, with voucher employed; these are described more
specimens preserved as necessary. fully in APHA (1992).
There is no intensive laboratory analysis
required. < Phytoplankton samples may be
obtained using water bottles
5.1.4 Phytoplankton deployed on a wire at a given, or
preferably various, depths. The
Phytoplankton are the base of most water bottles used should be
estuarine food webs (Day et al. 1989), constructed and cleaned in a manner
and fish production is linked to appropriate for the collection of
phytoplankton primary production (e.g., phytoplankton samples (e.g., Niskin
Day et al. 1989). Excessive nutrient and bottles washed and rinsed in order
organic inputs from human activities in to remove contaminants).
estuaries and their watersheds leads to Chlorophyll concentration is
eutrophication characterized by: measured from the sampled water,
reduction in seagrasses, increases in and phtyoplankton cells may be
phytoplankton biomass, macrophyte filtered or settled for identification
biomass (macroalgal biomass), reduced and enumeration.
water clarity, and reduced oxygen
saturation in bottom waters. From a

Table 5-7. Potential aquatic macrophyte metrics.
M etric Response to impairment
Tier 1:
% cover substantially more or less than reference
dom inant taxa substantially more or less than reference
Tiers 2-3:
% cover reduced or enhanced
biomass substantially more or less than reference
m aximu m depth of plant gro wth reduced under enrichment
density of new s hoots reduced
stem counts reduced
Table 5-8. Sampling summary for aquatic macrophytes.
Habitat Euphotic zone.
Sampling Gear Aerial photog raphy; quad rats
Index Period During growing season
Sampling Tier 1: Estimate of area covered by macrophytes.

Tiers 2 -3: Qu adrat sam ples fo r bio m ass co llected by diver; 3-5 random ly
placed trans ects perp endicular to sho re; sam ples are tak en at 0.5-m
depth inte rva ls fro m edge of em erg ent zone to th e sublittor al.
Analysis Tier 1: Dominant taxa identified, % cover estimated from aerial

pho tograp hy.
Tiers 2-3: All species identified, relative abundance of each estimated
from wet we ight.
Table 5-9. Sampling summary for phytoplankton.
Habitat Each sampling site preferred.
Sampling Gear Fluorom eter attache d to CTD (USE PA 19 94e) for in situ measurem ents;
or spectrophotometrically on water samples collected with a water
sam pler.
Index Period Tiers 1 and 2: June - September

Tiers 2 (optional) and 3: growing season average; 6-10 samples; March -
Octo ber (longer in sub tropical regions).
Sampling Preferred : single sam ple, 0.5-m depth.

Alternate: at same depths as nutrient samples.
Analysis Tier 1: Chloro phyll a mg /L (Tiers 1-3). Tier 2: ID dom inant taxa. Tier 3:
full comm unity species characterization.
< Phytoplankton may also be should, in general, be conducted at
collected by net hauls using a night. Also, consideration should be
plankton net with an appropriate given to the use of vertical or oblique
mesh size. tows. In any instance, gear size, mesh
size, rate of retrieval on the haul back,
Bottle collections are most useful vertical or oblique tow, time of day or
when analyzing a bulk community night and tide cycle are factors which
measure such as chlorophyll a must be kept constant if zooplankton
concentration (assuming a surveys are to be included in
fluorometer coupled to a CTD is not biocriteria development.
used), while net hauls are better for
studies designed to enumerate Meaningful bulk community
species. Water samples for measurements do not exist for
chlorophyll a determination can also zooplankton; therefore, if zooplankton
be used for nutrient analysis. are to be sampled, they should be
identified and enumerated. It may be
< The level of taxonomic difficult to locate or develop the
identification that should occur taxonomic expertise necessary to
will depend upon the diversity of identify zooplankton to species,
the community, the analyses that especially given the large number of
are to be performed, and the cost planktonic larvae. Zooplankton are
and availability of taxonomic considered to be in a developmental
experience; status with respect to their use as an
estuarine and coastal marine
< If phytoplankton are collected bioassessment assemblage.
using water bottles, the water may Zooplankton populations experience
be subsampled in the field or lab year-round seasonal fluctuations in
prior to analysis. The size and abundance as a result of variable
number of subsamples that should larval recruitment into the population,
be taken will depend upon the variable food sources, and physical
variability present in the processes which may move larvae and
community; adults into and out of the estuary (Day
et al. 1989). The pattern of seasonal
< If subsamples are taken from net abundance differs with changes in
hauls, it may be necessary to latitude. Zooplankton in higher
resuspend the organisms found in latitudes have one or more mid-
the cod end of the net in a larger summer peaks and very low numbers
volume of water in order to during the winter.
facilitate subsampling.
Abundances in temperate estuaries
5.1.5 Zooplankton are much more variable and may
(Developmental) experience spring peaks and minima
during the summer and winter
Zooplankton are most effectively months. Tropical estuaries do not
sampled using net hauls with 118-:m experience the low in population
mesh sizes. Because zooplankton are during the winter.
known to exhibit diel periodicity in
their locations in the water column, Some long-term monitoring projects
sampling times should reflect this have identified community measures
temporal variability; i.e., sampling that indicate changes in

environmental conditions over time the epibenthic community appear to
(e.g., nutrient loads or toxicants), as be persistent and sensitive to
well as particular zooplankton taxa environmental stress. They are
whose densities affect larval fish characterized by physiological
survival (Buchanan 1991). mechanisms that allow them to
Zooplankton community tolerate the varying salinity, DO, and
characteristics that are under temperature conditions encountered
investigation for application as in estuaries and coastal marine waters,
bioindicators include: or reproductive cycles that allow them
to avoid high-stress periods. Some
< Diversity, measured through epibenthos and facultative infauna
standard indexes such as can relocate to avoid areas of
Shannon-Wiener, to evaluate the environmental stress.
taxonomic complexity of the
assemblage; Epibenthos can be sampled using a
Renfro beam trawl, otter trawl, or
< Ratios of specific taxonomic epidbenthic sled. Camera tows or
groups within the assemblage to remotely operated vehicles with
gauge community balance and camera or video capabilities may also
identify possible impairment; allow enumeration of epibenthos,
although collection of organisms
< Presence of Hypotrichs (a ciliate of would not be possible and
the order Hypotrichida); quantitative assessments difficult.
Subsampling might involve a process
< Total biomass to assess similar to that suggested by Plafkin et
assemblage production; al. (1989); a box with a numbered grid
system into which collected
< Relative abundance of pollution epibenthos are evenly distributed
tolerant and sensitive species to could be used to randomly select an
identify and evaluate impairments appropriate number of organisms for
to the assemblage; subsequent sorting.
< Unnatural variability in Some of the advantages to using

abundance can be used to identify epibenthos for estuarine and coastal
the presence of short-term marine bioassessment are:
pollution or climate events;
< This assemblage is very sensitive
< Size structure can be used to to anthropogenic sources of stress,
evaluate the growth of cohorts in and it can be used in both a
the assemblage, which can nearfield and farfield context with
provide information on possible equal facility;
short- and long-term system
perturbations. Sampling can be conducted in shallow
waters using a dip net and in deep
5.1.6 Epibenthos (Developmental) waters with a trawl;
The epibenthos assemblage is also

considered to be in a developmental
stage for use in estuarine and coastal
marine bioassessment. Taxa within
< The total number of common < Seagrasses and macroalgae can
species will be limited by the fact hinder or increase the time
that the deep water sampling gear necessary for field sorting;
is restricted to fairly level bottoms;
< The seasonality of epifauna needs
< Subsampling can be employed to to be factored into the sampling
reduce labor costs and increase design.
cost-effectiveness;
The developmental method described
< Field and lab work, and data in Chapter 13 appears promising for
analyses can be done quickly with detecting impairment. If successfully
trained personnel; adapted to regions outside Florida,
North Carolina, and Puget Sound
< Samples can be sorted where it is being tested, it may
qualitatively, and a nonparametric become a standard estuarine
analysis can be applied to provide bioassessment method in the future.
a quick screening method. A proposed sampling protocol is
summarized in Table 5-10.
Table 5-10. Sampling summary for epibenthos.
Habitat Soft sedim ents (sleds an d trawls); shallow, veg etated (dip ne t)
Sampling Gear Re nfro B eam Tra wl (F arr ell 19 93a,b ), sm all otter trawl; epibenth ic sle d; d ip
net
Index Period Preferred: mid-summ er

Alternative: growing season, average of 10 samples.
Sampling Ca . 4-m tow length in es tua ries ; 0.1 - 0.5 nm tow length s (D GPS ) in
coastal waters and Puget Sound.
Analysis Taxonomic ID preferably to species.
The disadvantages of this assessment 5.1.7 Paleoenvironmental Systems

methodology are: (developmental)
< The stress index is developed Diatom and foraminifera species have
solely for anoxia; it might not narrow optima and tolerances for
allow assessment of other many environmental variables, which
stressors; make them useful in quantifying
environmental characteristics to a
< Stress values may not be available high degree of certainty. They
for many species, or may be immigrate and replicate rapidly,
difficult to determine; which makes them quick to respond
to environmental change (Dixit et al.
< Sleds and trawls are restricted to 1992). Changes in assemblages also
level bottoms; and cannot be used correspond closely to shifts in other
for sampling hard bottoms, or rock biotic communities sampled in
rubble; estuaries such as aquatic macrophytes,

zooplankton, and fish. They have also from each estuary or tributary being
been used alone as environmental assessed. However, once a
indicators of eutrophication, metal paleoecological record is established,
contamination, salinification, thermal there is no need to repeat the
effluents, and land use changes. sampling.
Furthermore, since diatoms and
foraminifera are abundant in almost Although the number of cores is
every marine ecosystem, a relatively small, each core requires substantial
small sample is sufficient for analysis. effort to analyze: sectioning,
This allows for many samples to be radioisotope dating, chemical
easily collected, analyzed, and analysis, pollen analysis for further
archived (Dixit et al. 1992). dating, and diatom or foraminifera
analysis. Current estimates for
The general lack of time-series data paleological analysis is about $100 per
has prompted attempts to section (not per core), depending on
demonstrate marine eutrophication the number and intensity of analysis
from present-day observations using done on each section and the
the benthic community and chemical experience of the lab performing the
criteria (Dale et al. 1999). Benthic analysis. The complexity of estuaries
foraminifera have been proven useful requires some background
as indicators of oxygen concentration information about the area in which
in bottom sediments (Alve 1991). sampling is occurring. This
Dinoflagellate cysts are also information should assist in decision
increasingly useful as indicators of making on the location and number of
short-term environmental change cores to be retrieved.
caused by climate and human
pollution (Dale et al. 1999). The cysts The study of paleoenvironmental
are recovered by pollen identification systems requires a corer that will
techniques; they are acid-resistant and retrieve an intact core, with minimal
therefore not subject to dissolution edge disturbance (Table 5-4). K-B,
problems sometimes affecting diatoms Phleger, and Piston corers have all
and foraminifera (Dale et al. 1999). been used successfully for these
Measurements of biogenic silica in analyses (see Section 5.1.1). Small
sediments are most often used as an surface area is not an issue; a single
index of diatom production (Stoermer core will suffice.
et al. 1990, Conley et al. 1993, Cooper
1995). Isolation of BSi from Si in 5.2 Sampling Design Issues
mineral phase is based upon the fact
that the silica of diatoms is only Consideration of sampling design is
weakly crystalline and dissolves critical in developing a new
readily in a weak base. Potential monitoring program for estuarine
indicators and a proposed sampling bioassessment and biocriteria.
summary are shown in Tables 5-11 Sampling design includes defining the
and 5-12. questions to be addressed by the data,
defining the units that will be
The total number of cores taken in a
particular estuary is dependent upon
the hydrological complexity of the
estuary. Generally, one to three cores,
but some times up to ten are required
Table 5-11. Potential paleoecological indicators
Indicator Response to Impairment Reference
Taxa richness (diatom, reduced Cooper and Brush 1991

foraminifera,
dinoflagellate cysts )
Biogenic silica increase with nutrient Turner and Rabalais 1994

enrichment
Total organic carbon, increase with enrichment Turner and Rabalais 1994
Total N, Total S
Ammonia/Elphidium increase with hypoxia Sen Gupta et al. 1996

ratio (foraminifera)
Centric/pennate ratio increase with nutrient Cooper and Brush 1991

(diatoms) enrichment
% Cyclotella increase with nutrient Cooper and Brush 1991

enrichment
sedimentation rate increase with watershed Brush 1989

erosion
Dinoflagellate cysts increase with cultural Dale et al. 1999

eutrophication
% Fursenkoina increases with hypoxia Alve 1991
% Trochammina increases with hypoxia Patterson 1990
Table 5-12. Sampling summary for paleoenvironmental systems
Habitat Stable depositional zone, biogeochemical conditions for preservation
Sampling gear Bottom corer
Index period None
Sampling Tiers 1-2: none
Tier 3: background information specific to the estuary being sampled will

determine the number of cores necessary.
Analysis Cores sectioned at regular intervals depending on deposition rate and

resolution desired.
Diatoms Species composition and enumeration of at least 300 organisms in each

Foraminifera section. Digestion/clarification methods depend on assemblage.
Dinoflagellate
Cysts
210
Age of sections Pb determination based on radioisotope assay with alpha
up to 150 years spectroscopy.
Older than 150 Palynological (pollen) analysis correlated with known historical changes
years in terrestrial vegetation (land use), and 14C analysis (>1000 yr).

sampled, and developing a sampling waters is similar to reference
design that is cost-effective for conditions? What percentage is
answering the defined questions. impaired?;
5.2.1 Statement of the Problem < Has estuary abc changed over a
certain period? Has it improved
The first task in developing a or deteriorated?;
sampling and assessment program is
to determine, and be able to state in < Overall, have estuarine waters in
simple fashion, the principal questions the region improved or
that the sampling program will deteriorated over a certain period?
answer. Questions may or may not be Have individual estuaries
framed as hypotheses to test, improved? Are more waters
depending on program objectives. For similar to reference conditions
example, suppose that a sampling now than some time ago?
program objective is to establish
reference conditions for biological Finally, resource managers often wish
criteria for estuaries in a given region. to determine the relationships among
Typically, the initial objectives of a variables, that is, to develop
survey designed to develop criteria predictive, empirical (statistical)
are to identify and characterize classes models that can be used to design
of reference sites in estuaries. Initial management responses to perceived
questions may then include: problems. Examples of specific
questions include:
< Should minimally disturbed sites
be divided into two or more < Can trophic state of an estuary be
classes that differ in biological predicted by areal nitrogen
characteristics and dynamics?; loading rate?;
< What are the physical, chemical, < Can biota of an estuary be
and relevant biotic characteristics predicted by watershed land use?
of each of the estuary site classes?
Monitoring and assessment data, and
After the monitoring and assessment derived models, may also be used to
program has developed biological help determine causal relationships
criteria, new questions need to be between stressors and responses of
developed that encompass systems. Inferring cause requires
assessments of individual sites, manipulative experiments, or
estuaries, or estuaries of an entire inference from multiple lines of
region or state. Specific questions evidence (Suter 1993). Since surveys
may include: and monitoring programs preclude
experimental investigations, inference
< Is site abc similar to reference sites of causal relations is beyond the scope
of its class (unimpaired), or is it of this document. Often, there is
different from reference sites (is it enough experimental evidence
altered or impaired)?; available from other studies so that
additional causal experiments are not
< Overall, what is the status of necessary and would be superfluous
estuarine waters in the region? (e.g., current knowledge of nutrients
What percentage of estuarine and trophic state generally makes it
unnecessary to “prove” 5.2.2 Definition of the Assessment
experimentally which nutrients are Unit
limiting). The development of
predictive models usually does not Defining the resource and assessment
require formal hypothesis testing. unit of the resource begins the process
of developing biological criteria. An
It is also necessary to specify the units “assessment unit” is a whole estuary
for which results will be reported. or part of an estuary, that will be
Usually, these units are the population assessed as meeting criteria, being
(e.g., all estuarine waters), but often impaired, etc. Clearly, a single square
subpopulations (e.g., embayments or meter where a grab sample is taken is
tributaries of a given estuary) and not large enough to be an assessment
even individual locations (e.g., sites of unit. An assessment unit should
special interest) can be used. In order consist of a definable segment, basin,
to help develop the sampling plan, it or entire estuary. For example, a large
is useful to create hypothetical complex estuary such as Puget Sound
statements of results in the way that could be divided into its component
they will be reported, for example: inlet bays, canals, and passes. Many
of the larger components could in turn
< Status of a place: Baltimore harbor is be divided into segments.
degraded;
Segmentation could be determined by
< Status of a region: 20% of the area some combination of mean salinity,
of Puget Sound has elevated trophic water residence time, dominant
state, above reference expectations; or substrate, or mean depth. For
20% of estuaries in Oregon have example, since estuarine fauna are
elevated trophic state; determined by salinity, segmentation
often corresponds to salinity zone
< Trends at a place: Benthic species (tidal fresh, oligohaline, mesohaline,
richness in Baltimore harbor has polyhaline, and marine). Small
increased by 20% since 1980; estuaries, such as salt ponds in New
England, could be single assessment
< Trends of a region: Average estuary units.
trophic state in New Jersey has
increased by 20% since 1980; or An assessment unit is the smallest
Average benthic index values in 20% spatial subdivision of an estuary that
of estuaries of the west coast have will be assessed; i.e., given a rating of
increased by 15% or more since 1980; good or poor. An assessment may be
based on one or more sample units
< Relationships among variables: within an assessment unit. A sample
50% increase of N loading above unit (or sample site) is a site where an
natural background is associated with observation is made.
decline in taxa richness of benthic
macroinvertebrates, below reference 5.2.3 Specifying the Population
expectations; or Estuaries receiving and Sample Unit
runoff from large urban areas have
50% greater probability of elevated Sampling is statistically expressed as a
trophic state above reference than sample from a population of objects.
estuaries not receiving such runoff. Thompson (1992) suggested in some
cases, the population is finite,

countable, and easy to specify, (e.g., < An estuary or a definable portion
all persons in a city, where each of the estuary as a single sample
person is a single member of the unit. Whole estuaries as sample
population). In estuaries, the units would only be used in very
population is often more difficult to broad-scale regional assessments,
specify and may be infinite, (e.g., the as was done by EMAP-NC, for
sediment of San Francisco Bay, where example, for small estuaries as a
any location in the Bay defines a population (e.g., Strobel et al.
potential member of the population). 1995).
Sampling units may be natural units
(entire estuaries, cobbles on a beach), 5.2.4 Sources of Variability
or they may be arbitrary (plot,
quadrat, sampling gear area or Variability of measurements has many
volume) (Pielou 1977). Finite possible sources, and the intent of
populations may be sampled with many sampling designs is to minimize
corresponding natural sample units, the variability due to uncontrolled or
but often the sample unit (say, an random effects, and conversely to be
estuary) is too large to measure in its able to characterize the variability
entirety, and it must be characterized caused by experimental or class
with one or more second stage effects. For example, we may stratify
samples of the sampling gear (bottles, estuarine waters by salinity and
benthic grabs, quadrats, etc.). bottom substrate type (rocky, sandy,
muddy). Typically, we stratify so that
The objective of sampling is to best observations (sample units) from the
characterize individual sample units same stratum will be more similar to
in order to estimate some attributes each other than to sample units in
(e.g., nutrient concentrations, DO) and other strata.
their statistical parameters (e.g., mean,
median, variance, percentiles) of a Environmental measures vary across
population of sample units. The different scales of space and time, and
objective of the analysis is to be able to sampling design must consider the
say something (estimate) about the scales of variation. When sampling
population. Examples of sample units estuaries, measurements (say, benthic
include: assemblages) are taken at single
points in space and time (1 point
< A point in an estuary (may be along a transect in mid-summer). If
characterized by single or multiple the same measurement is made at a
sample device deployments). The different place (littoral zone),
population would then be all embayment, or time (winter), the
points in the estuary, an infinite measured values will likely be
population. This is the most different. A third component of
common sample unit applied to variability is the ability to accurately
estuarine assessments; measure the quantity interested in,
which can be affected by sampling
< A constant area, (e.g., square gear, instrumentation, errors in proper
meter, hectare). The population adherence to field and laboratory
would be an artificial one protocols, and the choice of methods
consisting of all square meters of used in making determinations.
estuarine surface area in an
estuary, a state or a region;
The basic rule of efficient sampling measured more than once to estimate
and measurement is to sample so as to measurement error.
minimize measurement errors; to
maximize the components of If the variance of individual
variability that have influence on the measurements (measurement error) is
central questions and reporting units; unacceptably large; i.e., as large or
and to control other sources of larger than variance expected among
variability that are not of interest, that sample units, then it is often necessary
is, to minimize their effects on the to alter the sampling protocol, usually
observations. Many locations are by increasing sampling effort in some
sampled in order to examine and way, to further reduce the
characterize the variability due to measurement error. Measurement
different locations (the sampling unit). error can be reduced by multiple
Each site is sampled in the same way, observations at each sample unit, (e.g.,
in the same place, and in the same multiple dredge casts at each
time frame to minimize confounding sampling event, multiple observations
variability. in time during a growing season or
index period, depth-integrated
In statistical terminology, there is a samples, or spatially integrated
distinction between sampling error samples.
and measurement error that has little
to do with actual errors in A less costly alternative to multiple
measurement. Sampling error is the measures in space is to make spatially
error attributable to selecting a certain composite determinations. In nutrient
sample unit (e.g., an estuary or a or chlorophyll determinations, a water
location within an estuary) that may column pumped sample, where the
not be representative of the pump hose is lowered through the
population of sample units. Statistical water column, is an example of a
measurement error is the ability of the spatially composite determination.
investigator to accurately characterize Spatial integration of an observation
the sampling unit. Thus, and compositing the material into a
measurement error includes single sample is almost always more
components of natural spatial and cost-effective than retaining separate,
temporal variability within the sample multiple observations. This is
unit as well as actual errors of especially so for relatively costly
omission or commission by the laboratory analyses such as organic
investigator. Measurement error is contaminants and benthic
minimized with methodological macroinvertebrates. Many estuarine
standardization: selection of cost- programs have adopted sampling
effective, low variability sampling protocols consisting of multiple grabs
methods, proper training of at a site that are then composited into
personnel, and quality assurance a single bucket for laboratory
procedures to minimize determinations (e.g., EMAP Near
methodological errors. In analytical Coastal: 3 composited Van Veen grabs
laboratory procedures, measurement at each site; Holland 1990).
error is estimated by duplicate
determinations on some subset of Statistical power is the ability of a
samples (but not necessarily all). given hypothesis test to detect an
Similarly, in field investigations, some effect that actually exists, and must be
subset of sample units should be considered when designing a

sampling program (e.g., Peterman variables such as nutrient
1990, Fairweather 1991). The power of concentrations, loadings, or
a test (1-β) is defined as the chlorophyll concentrations of
probability of correctly rejecting the estuaries. Designs that assume that
null hypothesis (H0 ) when H0 is false; the observed variables are themselves
i.e. the probability of correctly finding random variables are model-based
a difference [impairment] when one designs, where prior knowledge or
exists. For a fixed confidence level assumptions (a model) are used to
(e.g., 90%), power can be increased by select sample units.
increasing the sample size or the
number of replicates. To evaluate Probability-based designs (random
power and determine sampling effort, sampling)
an ecologically meaningful amount of
change in a variable must be set. See The most basic probability-based
Chapter 12 for a discussion of design is simple random sampling,
statistical power, and examples. where all possible sample units in the
population have the same probability
Optimizing sampling design requires of being selected, that is, all possible
consideration of tradeoffs among the combinations of n sample units have
measures used, the effect size that is equal probability of selection from
considered meaningful, desired among the N units in the population.
power, desired confidence, and If the population N is finite and not
resources available for the sampling excessively large, a list can be made of
program. Every study requires some the N units, and a sample of n units is
level of repeated measurement of randomly selected from the list. This
sampling units to estimate precision is termed list frame sampling. If the
and measurement error. Repeated population is very large or infinite
measurement at 10% or more of sites (such as locations in an estuary), one
is common among many monitoring can select a set of n random (x,y)
programs. coordinates for the sample.
5.2.5 Alternative Sampling All sample combinations are equally

Designs likely in simple random sampling,
thus there is no assurance that the
Sampling design is the selection of a sample actually selected will be
part of a population to observe the representative of the population.
attributes of interest, in order to Other unbiased sampling designs that
estimate the values of those attributes attempt to acquire a more
for the whole population. Classical representative sample include
sampling design makes assumptions stratified, systematic, multistage, and
about the variables of interest, in adaptive designs (Figure 5-2). In
particular, it assumes that the values stratified sampling, the population is
are fixed (but unknown) for each subdivided or partitioned into strata,
member of the population, until that and each stratum is sampled
member is observed (Thompson 1992). separately. Partitioning is typically
This assumption is perfectly done so as to make each stratum more
reasonable for some variables, say, homogeneous than the overall
length, weight, and sex of members of population. Systematic sampling is
an animal population, but it seems the systematic selection of every kth
less reasonable for more dynamic unit of the population from one or
Figure 5-2
Sampling Methods
Description of
various sampling
Simple Random: Samples are independently located methods.
at random Adapted from
USEPA 1992.
Systematic: Samples are located at regular

intervals
Stratified: The study area is divided into

nonoverlapping strata and samples
are obtained from each
Multistage: Large primary units are selected

which are then subsampled
more randomly selected starting units, Model-based designs

and ensures that samples are not
clumped in one region of the sample Use of probability-based sampling
space. Multistage sampling requires designs may miss relationships
selection of a sample of large primary among variables (models), especially
units, such as fields, hydrologic units, if there is a regression-type
rectangles, or hexagons, and then relationship between an explanatory
selection of secondary sample units and a response variable. As an
such as plots or estuaries within each example, estimation of benthic
primary unit in the first stage sample. response to discharge or outfalls
requires a range of sites from those
Estimation of statistical parameters directly adjacent to the outfalls to
requires weighting of the data with those distant from, and presumably
inclusion probabilities (the probability unaffected by, the outfalls (e.g.
that a given unit of the population Warwick and Clarke 1991). A simple
will be in the sample) specified in the random sample of estuarine sites is
sampling design. In simple random not likely to capture the entire range,
sampling, inclusion probabilities are because there would be a large cluster
by definition equal, and no corrections of far sites, with few at high ends of
are necessary. Stratified sampling the gradient. A simple random
requires weighting by the inclusion sample may therefore be highly
probabilities of each stratum. inefficient with respect to models or
Unbiased estimators have been specific hypotheses.
developed for specific sampling
designs, and can be found in sampling In model-based designs, sites are
textbooks, such as Thompson (1992). selected based on prior knowledge of
auxiliary variables, such as estimated
loading, depth, salinity, substrate

type, etc. These designs preclude an of test sites may vary from one to
unbiased estimate of the state of the several depending on the purpose of
estuaries, unless the model can be the study. The distance between
demonstrated to be robust and stations could be decreased; i.e.,
predictive, in which case the number of stations increased to
population value is predicted from the partially account for the inefficiency of
model and from prior knowledge of some sampling gear or, conversely,
the auxiliary (predictive) variables. the distance increased; i.e., number of
Selection of unimpacted reference stations decreased once the data have
sites is an example of a model-based been evaluated.
design which cannot later be used for
unbiased estimation of the biological Index Period
status of estuaries. Ideally, it may be
possible to specify a design that Most monitoring programs do not
allows unbiased estimation of both have the resources to characterize
population and model, with an variability or to assess for all seasons.
appropriately stratified design. Sampling can be restricted to an index
Statisticians should be consulted in period when metrics are expected to
developing the sample design for a show the greatest response to
biological criteria and monitoring pollution stress and when within-
program. season variability is small (Holland
1990). A decision must be made
Selecting a Design between selecting a sampling period
that is representative of the biological
The selection of a station array for community, or one that reflects the
bioassessment will depend on the worst-case conditions for pollution
nature of the study and/or the desire stress. From the traditional
to delineate the areal extent of perspective of evaluating pollution
impairment. A randomized station impacts in fresh water streams,
selection is most appropriate for summer-time low flow conditions are
environmental status and trends often chosen to assess effects from
surveys such as conducted by EMAP. point source discharges. These flow
However, for specific management conditions represent minimal effluent
decision-making, pre-selected stations dilution in combination with the
placed on a gradient such as distance natural stressors of low water velocity
from of a discharge (sometimes and high temperature in those
termed "nearfield/farfield") may be constrained environments. In
more appropriate. This method is a contrast, the effects of nonpoint source
form of model-based design, and pollution on the benthic community
more accurately identifies suspected are often evaluated following periods
sources of impairment, assesses of high flow since nonpoint source
impacts and monitors recovery. effects on aquatic communities are
largely driven by runoff in the
The number of stations to be watershed. Estuaries and coastal
incorporated in a study design is most waters accumulate materials from
heavily influenced by the available both nonpoint and point sources in a
resources. A minimum of three much more dynamic way and thereby
control or reference sites is desired to confound the assessment so useful for
provide some indication of streams.
background variability. The number
In bioassessment strategies involving alternative sampling scheme. See
infrequent sampling, the biologically- Chapter 12 for a more detailed
optimal period for sampling becomes discussion of statistical power. The
a major consideration. Periods of various sampling schemes consist of
instability in community structure, different combinations of sampling
including recruitment of young, gear, gear area, sieve mesh size, and
natural harsh environmental number of replicates. The method
conditions, changes in food source, allows determining the optimum
and migration of certain target among a set of sampling schemes for
populations are all considerations in detecting differences in reference vs.
conducting these biosurveys. The impaired stations when the statistical
biologically-optimal period, usually model is a t-distribution for
mid-summer and sometimes mid- comparing two means. The optimum
winter, avoids all of these elements scheme can be defined as the least
and focuses on the time when costly one capable of reliably (e.g., " =
communities are most stable. The 0.5, 1-$ = 0.95) detecting a desired
resource manager or biologist will difference in the means of a metric
have to choose between these between two stations. The approach
conditions, or select to cover both, can be applied to each metric in a test
depending on the needs of the study. set of metrics and the results
aggregated to determine the optimum
5.2.6 Optimizing Sampling protocol.
Ferraro et al. (1994, 1989) present a There are four primary steps in
method for quantitatively evaluating assessing the PCE of a suite of
the optimum macrobenthic sampling alternative sampling schemes:
protocol, accounting for sampling unit
area, sieve mesh size, and number of 1. For each scheme, collect replicate
replicates (n). Their approach allows samples at paired reference and
managers responsible for designing impaired stations. The observed
and implementing estuarine and difference in metric values
coastal marine bioassessment between the stations is
programs to answer fundamental operationally assumed to be the
questions: magnitude of the difference
desired to be detected.
< How large should the sampling Alternatively, a percentage of the
unit be?; median (e.g., 20%) for a given
metric calculated across reference
< What sieve mesh size should be stations could be set as the
used?; magnitude of the difference to be
detected. In either case, this
< How many replicate samples difference, divided by the
should be taken? standard deviation, is the “effect
size” (ES) of interest.
The procedure calculates the “power-
cost efficiency” (PCE), which 2. Assess the “cost” (ci), in time or
incorporates both the number of money, of each sampling scheme i
samples (n), the cost (field collection at each station. The cost can
effort and lab effort combined) and include labor hours for sampling,
the expected statistical power for each

sorting, taxonomic identification,
and recording results.
3. Conduct statistical power analysis

to determine the minimum
number of replicate samples (ni)
needed to detect the ES with an
acceptable probability of Type I (")
and Type II ($) error (e.g., " = $ =
0.05).
4. Calculate the power-cost efficiency

(PCE) for each sampling scheme
by:
PCEi = (n x c)min /(ni x ci)
where (n x c)min = minimum value

of (n x c) among the i sampling
schemes. The reciprocal of PCEi is
the factor by which the optimal
sampling scheme is more efficient
than alternative scheme i. When
PCE is determined for multiple
metrics, the overall optimal
sampling protocol may be defined
as that which ranks highest in PCE
for most metrics in the test set.
Chapter 6
Water Column & Bottom
Characteristics
Tiers 1-3 contain active survey and site decimeters. The disk is lowered into the
sampling. Procedures for attaining water until it disappears from view and
water column and bottom characteristics the depth is recorded. The disk is then
are generally the same for each tier. The slowly raised to the point where it
sampling however, occurs more often reappears, with the depth being
over the year. Differences are noted recorded again. The mean of these two
where applicable. Table 6-1 compares measurement is the Secchi depth.
the level of effort for each tier. Observations are made from the shady
However, agencies will decide which side of the boat, without sunglasses, and
components of each tier will be as close as possible to the water to
incorporated into their specific reduce glare.
programs, then they will select the level
of effort appropriate for their program. 6.3 Depth
6.1 Salinity, Temperature, Depth should be measured at each

Dissolved Oxygen, & pH station using a calibrated depth sounder.
Depth can be read off a meter block
Salinity, conductivity, temperature, when sediment sampling by zeroing the
dissolved oxygen, and pH should be block when the sampler is at the water
measured at each sampling station using surface. In shallow, inshore waters, a
a CTD meter equipped with DO and pH long stick or weighted line calibrated in
probes. Measurements should be made decimeters may be used.
at 1-m intervals through the water
column. In shallow, inshore waters, 6.4 Sediment Grain Size
measurements should be taken at the
top, middle, and bottom thirds of the 6.4.1 Estimation of “percent fines”
depth. For Tier 3, in some southern (Tier 1)
waters that undergo significant diel
temperature changes, it may be Analysis of sediment grain size for Tier
desirable to obtain 24-hour temperature 1 assessments can be limited to
profiles using recording equipment. determining the “percent fines” at each
station. A rapid wet sieving technique
6.2 Secchi Depth used in Puget Sound (Eaton 1997) can
serve as the basis for this
Secchi depth is usually measured at the characterization. Materials needed for
deepest part of the transect or grid. the procedure include:
Where the area is classified by depth,
Secchi measurements should be made at < standard testing sieve No. 230, 63-
each station. Readings are obtained :m
with a 40-cm plastic or metal Secchi disk < 50-ml plastic beaker (filled to the
that is either white or is divided into brim with sediments is about 79-ml)
black and white quadrants on a < 100-ml plastic graduated cylinder
nonstretchable line that is calibrated in < water bottle(s) with small outlets
Table 6-1. Water Column & Bottom Characteristics. “Addition” refers to added detail or intensities
for a parameter initiated in an earlier tier.
Characteristic Tier Collection Method Indicates
1 -measure at each sampling station, CTD Distribution of flora and
2 meter fauna
Salinity
3 -continuous or 1-2-m intervals through
water column
-shallow/inshore
-top, middle, bottom thirds of depth
1 -measure at each station, CTD meter Rate of chemical
2 -1-2-m intervals through water column reactions and biological
Temperature
-shallow/inshore processes
-top, middle, bottom thirds of depth
3 -some southern waters undergo significant
addition diel changes, it may be desirable to obtain
24-hour temperature profiles
1 -measure at each station, CTD meter w/ Possible reason for
DO probe modified behavior,
-continuous or 1-2-m intervals through reduced abundance &
water column productivity, adverse
-shallow/inshore reproductive effects,
Dissolved Oxygen
-top, middle, bottom thirds of depth and mortality

2 -measure early in morning at each station
addition at minimum
3 -collect along a depth profile from surface Resource agency may

addition to within 1-m of bottom at 1-2-m intervals determine need for
-in cases of hypoxic site: recording DO more detailed
meters may be deployed (EMAP - information to diagnose
Louisianian Province, Engle et al 1994) sources & causes of
impairment
1 -CTD w/ pH probe Chemical condition,

2 -1-2-m intervals pollutant input, high
pH
3 -top, middle, bottom thirds of depth concentrations of

phytoplankton
1 -deepest part of transect/grid Reduction of light
Secchi Depth
penetration, deposition
(Turbidity)
2 -if area classified by depth, measure at

3 each station of mud and silt,
-See Section 6.2 for complete procedure possible contaminated
sediment “hot spots”
1 -each station w/ calibrated depth sounder Depth at sampling

2 -read off meter block when sediment station, possible
Depth
3 sampling dredging or sediment

-shallow/inshore waters: long stick or loading
weighted line calibrated in decimals
Nutrients
2 -collected w/ bottle samplers or pump Nutrient loading

3 -see Section 6.8 for complete procedure
3 -each station during index period, and any Bottom characteristics,

Acid Volatile
other sampling visits through year detailed purposes in

-once accurate AVS exists for each Section 3.5.4
Sulfides
station, analytes only performed once per

year (during index period)
3 Choose One: Trace distribution of

Water Column
-USEPA’s list of Priority Pollutants, contaminants from a

Contaminants
Hazardous Substance, or Target source or to ID

Compound/Analytes potential sources
-same compounds targeted in EMAP-E
(Table 3-1)
-develop own list (see Section 6.10 for
more detail)
6-2 Water Column & Bottom Characteristics

Table 6-1 (Cont’d). Water Column & Bottom Characteristics. “Addition” refers to added detail or
intensities for a parameter initiated in an earlier tier.
Characteristic Tier Collection Method Indicates

1 -determine “percent fines” at each station, Spatial and temporal
see Section 6.4.1 for complete procedure changes of the benthic
habitat, evaluate
condition of benthic
Sediment Grain Size
habitats
2 -see Section 6.4.2 for complete procedure Determine extent or
recovery from
environmental
perturbations
3 Assist in providing early
warnings of potential
impacts to the
estuarine ecosystem
2 -see Section 6.9 for complete procedure Provide information
regarding sediment
organic content
Total Organic
(possibly influenced by
sewage outfalls)
Carbon
3 -measure additional sediment analytes Examine potential

addition influences of outfalls,
ID potential
contaminant “hot spots”
1 -vertical bisection, distance from sediment Note presence/absence
RPD Layer Depth
surface to a noticeable change in color of benthos; learn about

from brownish (oxidizing conditions) to life history, taxa
gray (reducing conditions) abundance, & major
taxa biomass
distribution; more large,
deep dwelling
species=”healthy”
system
1 -deepest section along transect/grid Sediment and carbon
Total Volatile
-see Standard Methods (APHA 1992) for content

sampling & analytical methods
Sulfides
1 -conducted at outset of survey Positive=severe

impacts influence
spatial sampling
design, causal
investigations
Negative=subsequently
Sediment Contaminants
collected biological info.

2 *like TOC, if toxicity tests are initially essential to ID other,
negative, no need to repeat annually possibly more subtle
unless biological data from infauna stresses
indicate otherwise Provide insight on
limiting factors in
benthic community
3 Choose from three approaches:

-based on EPA’s contaminant lists
-NOAA NS&T suite of contaminants (used
by EMAP)
-targeted list
*see Section 6.12 for complete procedure
and rationale
< small stainless or plastic spatula original volume to obtain the percentage
< stainless butter knife of the coarse fraction. The standard
< hose with nozzle (if running water is usage, however, is for percent fine-
available). grained fraction or “percent fines”.
This is calculated by subtracting the
Detailed directions for performing this volume of sediment remaining in the
wet-sieving technique are as follows: cylinder (ml of coarse-grained fraction)
from the original volume, and dividing
Fill a 50-ml plastic beaker to the brim this number (ml of fine-grained) by the
with the sediment to be analyzed. The original volume to obtain the percent
capacity of the completely filled beaker fines.
can be measured using water and the
100-ml graduated cylinder. Clean away 6.4.2 Sediment Grain Size (Tiers 2
any sediment that might adhere to the and 3)
outside of the beaker. Carefully wash
this sediment through a 63-:m standard Additional grain size data for Tier 2 and
sieve (USA standard testing sieve No. Tier 3 assessments should include
230) with stainless steel mesh. The sieve determination of the size distribution
itself is about 9" in diameter with a 2" using a standard graded sieve series.
stainless lip. Be careful not to overflow This analysis should be performed for a
the sieve with rinsing water. It may be sediment sample collected at each
easier to wash half of the sediment sampling station. In the early years of
through at a time. If running water is the assessment program, this analysis
available, use a small brass nozzle on the should be performed for each sampling
end of the hose with very low water period. When an accurate sediment
pressure when washing the sediment, characterization exists for the area of
otherwise the sediment will need to be each station, sediment grain size
washed using the water bottle. If there analysis could be performed only
are occasional large worm tubes or annually or biennially (on samples
shells, these are discarded and replaced collected in the index period), unless the
with an approximately equal volume of agency believed that sediment
sediment. The sediment remaining on conditions at a site may have changed.
the sieve is the coarse-grained fraction. This could occur, for example, following
This is washed to one side of the sieve, a major storm. Buller and McManus
and then carefully placed into the plastic (1979) provide a review of the
100-ml graduated cylinder with a methodological and statistical analysis
stainless steel butter knife, and finally of sediment samples. If seasonal
with the small stainless spatula. The variations in grain size are exhibited, it
water bottle is then used to wash any is recommended that direct comparisons
remaining sediment directly into the between samples collected during
graduated cylinder, and to wash down different seasons be avoided. Studies
the sides of the cylinder. Let the investigating interannual variation in
sediment-water mixture settle in the the percent composition of grain sizes
100-ml graduated cylinder for should be conducted during the same
approximately 5 minutes until the season (preferably the same month) each
supernatant water is clear. This may year. Furthermore, it is recommended
take longer for very fine-grained that grain size be sampled when
sediments. Note the volume of the contaminant concentrations are expected
coarse-grained fraction which remains to be at their highest level to evaluate
after sieving. This can be divided by the worst-case scenarios.

6.5 RPD Layer Depth short term adverse effects of potentially
contaminated sediment, or of a test
The concept behind using the depth material experimentally added to
distribution of benthic sediment, on marine or estuarine
macroinvertebrates is based on the infaunal amphipods during static 10-day
premise that “healthy” benthic exposures for the following species:
communities in fine sediments in meso- Rhepoxynius abronius, Eohaustorius
and polyhaline waters consist of estuaris, Ampelisca abdita, Grandidierella
relatively large, deep dwelling species; japonica, and Leptocheirus plumulosus.
while impaired areas will have fewer of The amphipod Corophium insidiosum has
these organisms. The depth distribution also been used in standard testing (Reish
of benthic infauna in sediments and Lemay 1988). Solid phase tests use
integrates functional parameters such as overlying water in aerated 1-L glass test
life history, taxa abundance, and major chambers. Mortality and sublethal
taxa biomass distribution. effects such as growth, emergence of
adults, and inability to bury in clean
sediment are determined after exposure
6.6 Total Volatile Solids
of a specific number of amphipods
Total volatile solids (TVS) is the Tier 1 (usually 20) to the test sediment.
indicator for sediment carbon content. Response of the amphipods to the test
TVS should be determined for the sediment is compared with the response
deepest station along each transect or observed in control or reference
grid, based on the assumption that sediment. The negative control
deeper stations will represent sinks for sediment is used to provide a measure
organic carbon in the sediments. of the acceptability of the test by
Sampling and analytical methods are providing evidence of the health and
discussed in Standard Methods (APHA relative quality of the test organisms, the
1992). suitability of the overlying water, and
test conditions and handling procedures
(ASTM 1998b, USEPA 1994b). The
6.7 Sediment Contaminant reference sediment, which is similar in
Toxicity physical characteristics to the test
sediments and typically collected from a
Sediment toxicity testing is a diagnostic similar location, is used as the basis for
indicator for Tier 3. When results are interpreting data obtained from the test
positive for a station, severe impacts at a sediments (ASTM 1998b).
known locality will influence spatial
sampling design and causal The toxicity of field-collected sediments
investigations. Where toxicity test may be assessed by either (a) testing the
results are negative throughout the set whole sediment and testing for
of stations sampled, subsequently significant differences in responses
collected biological information is between reference or control and test
essential to identify other, possibly more sediment exposed animals or (b) testing
subtle stresses on the system. dilutions of a test sediment with clean
sediment to obtain an LC50 or other
6.7.1 10-day Static Sediment effect concentration, for survival,
Toxicity Test with Marine and reburial success, or growth (ASTM
Estuarine Amphipods 1998b, Nelson et al. 1993, Swartz et al.
1995).
ASTM (1998a) and USEPA (1994b)
developed procedures that measure
6.7.2 10-day Static Sediment exposed to negative control or reference
Toxicity Test with Marine and sediment in 20- to 28-day tests. The
Estuarine Polychaetous toxicity of field sediments may also be
Annelids assessed by testing dilutions of highly
toxic test sediments with clean
Marine or estuarine infaunal sediments to obtain either an LC50 or
polychaetes are used in whole sediment other effect concentration of the
tests during 10-day or 20- to 28-day material.
exposures to determine adverse effects
of potentially contaminated sediment, or 6.7.3 Static Acute Toxicity Tests
of a test material added experimentally with Echinoid Embryos
to sediment. Polychaete species include
Neanthes virens for the 10-day and Echinoderm embryos and larval form
Neanthes arenaceodentata for the 10-day sea urchins (Strongylocentrotus
and 20- to 28-day tests (ASTM 1998c). purpuratus and Strongylocentrotus
Other polychaete species that have been droebachiensis) and sand dollars (Arbacia
used in similar sediment testing include punctulata, Lytechinus pictus, and
Capitella capitata, Ophrotrocha diadema, Dendraster excentricus) have been used in
and Ctenodrilus serratus (Reish and marine sediment interstitial (pore) water
Lemay 1988). The 10-day test measures tests (ASTM 1998a). Interstitial water
effects of contaminated sediment on from marine sediments is isolated using
polychaete survival. The 20- to 28-day either in-situ peepers (Sarda and Burton
test determines effects of contaminated 1995, Brumbaugh et al. 1994, Bufflap and
sediment on polychaete survival and Allen 1995), suction in the field (Watson
growth. If smaller species are used, such and Frickers 1990), laboratory
as N. arenaceodentata, five worms are centrifugation (Ankley et al. 1991,
placed in a 1-L glass test chamber with a Burgess et al. 1993, Kemble et al. 1994,
minimum sediment depth of 2- to 3-cm ASTM 1998b), or sediment squeezing
and the overlying water is aerated. (Long et al. 1990). Embryos are obtained
Either young adults or recently emerged by inducing adults to spawn, using
juvenile (2- to 3-weeks post-emergence) either physical (e.g., electric stimuli) or
worms are used in the 10-day test; only chemical (injection of potassium
recently emerged (2- to 3-weeks) chloride) means, and then combining
juveniles are used in the 20- to 28-day gametes.
test. Survival of worms exposed to the
test sediment is compared with the Embryos are exposed to the test pore
survival in a negative control or water and controls (culture water) for
reference sediment in either test. If 48- to 96-hours, depending on the
larger species are used, such as N. virens, species and test temperature. The test
ten worms are placed in a glass aquaria measures the proportion of embryos or
(4- to 37-L) with a minimum sediment larvae that develop into normal pluteus
depth of 10-cm and the overlying water larvae. Pore waters can be tested
is aerated. “whole”; i.e., undiluted, and organism
responses expressed in terms of a
The percent survival of polychaetes significant difference between controls
exposed to field-collected sediment is and test waters. Alternatively, pore
compared to those exposed to a negative water samples can be diluted with
control or reference sediment in 10-day known, clean culture water and the
tests. Survival and body weight of results expressed as an LC50 or other
surviving animals is compared to those

effect concentration with confidence larvae are examined and the percentages
limits. of mortality and abnormal survivors are
determined and analyzed.
6.7.4 Toxicity Tests Using Marine
Bivalves 6.8 Nutrients (Tiers 2&3)
Juveniles of the marine bivalve species, Water column samples for nutrient
Mulinia lateralis, have been used in analysis can be collected using bottle
whole sediment tests (Burgess and samplers such as Kemmerer, Van Dorn,
Morrison 1994). Juveniles are exposed Niskin, or Nansen samplers. A pump
for 7-days to determine adverse effects may be used as an alternative sampling
of potentially contaminated sediment, or device. In shallow water less than 2-m
of a test material added to sediment. depth, a mid-depth sample at each
Bivalve responses measured include station should be obtained for nutrient
survival and growth, (total organism analysis. In waters greater than 2-m
dry weight). Ten juvenile bivalves (four depth, samples should be collected at
weeks old) are placed into six replicate each station at 1-m below the surface, 1-
chambers per sediment or treatment. m above the bottom, 1-m above the
The sediment exposure chambers are pycnocline, 1-m below the pycnocline,
prepared by placing approximately 1.0- or at mid-depth. Analytical methods for
cm deep sediment into 150-ml dishes, NH4 -N, NO3 -N, NO2 -N, Kjeldahl
followed by the addition of 100-ml nitrogen, total N, and total and reactive
filtered 30-gkg-1 seawater. Upon P; i.e., ortho-P, are presented in APHA
initiation of the test a subsample of (1992) and USEPA (1994c). These
organisms are set aside for nutrient analyses will help identify
determination of initial juvenile weights. eutrophication factors affecting
Bivalve survival in test chambers is biocriteria development, as well as
compared to survival of bivalves in the supplement the USEPA’s nutrient
negative control or reference sediment. criteria initiatives so that multiple
Dry weight of the surviving organisms objectives can be accomplished at once.
in test chambers is compared with dry
weight of surviving organisms in the 6.9 Total Organic Carbon
reference sediment, and to the dry
(Tiers 2&3)
weight of the subsample set aside at the
initiation of the test to determine
In Tier 2, the primary purpose of
growth.
measuring total organic carbon (TOC) is
to provide information regarding
Similar to echinoderm testing
sediment organic content, which might
summarized in Section 6.7.3, bivalve
be influenced by sewage outfalls
larvae have also been used in sediment
containing high organic levels. As noted
pore water and sediment elutriate
in Chapter 3, TOC in the sediment is an
toxicity tests. Species used include
important analyte for the purpose of
Crassostrea gigas and Mytilus edulis
evaluating the bioavailability of organic
(PSEP 1995). Bivalve larvae are obtained
pollutants and metals adsorbed by
from laboratory-cultured adult brood
sediments or contained in sediment
stock, which are induced to spawn.
porewater. Data on sediment TOC
Developing embryos are exposed to the
collected in this tier can be used to
pore water or elutriate at 20°C for 48-60-
examine potential influences of outfalls
hours using static-test conditions. At
in addition to potential sediment
test termination, subsamples of the
contaminant “hot spots” that can be
assessed in Tier 3 with the measurement this information also include NPDES
of additional sediment analytes. permit records and discharger toxicity
test results. In any case, three replicate
Standard methods for TOC analysis are water samples should be collected at
presented in APHA (1992). In the early each sampling station within an
years of the assessment program, TOC appropriate index period and on at least
analysis should be performed for each three other visits during the year to
station in each sampling period. Once capture temporal variations in
the resource agency is confident that an contaminant concentrations. Historic
accurate characterization of sediment water contaminant data, plus data
TOC exists for each station, the analysis collected in this tier, can be used by the
could be performed only once every two state to determine a more limited list of
or more years (on samples collected in analytes for subsequent years of the
the index period), unless stations that assessment and biocriteria program.
appear to be influenced by organic input
(e.g., sewage outfalls) are identified. In The same type of sampling bottle used
this case, TOC analysis should continue to collect water samples for nutrient
to be performed for each sampling analysis may be used for contaminant
period for these stations. samples. USEPA (1992) and APHA
(1992) contain detailed information on
6.10 Water Column analytical methods.
Contaminants (Tier 3)
6.11 Acid Volatile Sulfides
Water column contaminants such as (Tier 3)
organic compounds (e.g., herbicides,
pesticides, hydrocarbons) and metals Details of the purposes for measuring
may be important indicators of sources acid volatile sulfides (AVS) present in
and causes of impairment to biological bottom sediments are provided in
assemblages in estuaries and coastal Section 3.5.4. Given the diagnostic
marine waters. Decisions on which intent of a Tier 3 assessment, it is
chemicals to include in Tier 3 important to include this analyte in
assessments can be difficult. Three determinations of bottom characteristics
approaches to selecting contaminants only if metals are suspected as a cause of
might be useful. One approach would biological degradation. Allen et al.
be to analyze for all chemicals listed on (1993) discuss analytical methods for
USEPA’s Priority Pollutant, Hazardous this parameter. AVS measurements
Substance, or Target Compound/ should be made on sediment samples
Analyte Lists. A second approach collected at each station during an
would be to analyze for the same appropriate index period and any other
compounds targeted in the EMAP- sampling visits made throughout the
Estuaries program (refer to Table 3-1). A year. Once the resource agency is
third approach would be to develop a confident that an accurate
targeted list. In this latter approach, the characterization of sediment AVS exists
historical information from Tier 0 and for each station, the analytes should be
subsequent follow-up inquiries of land performed only once per year (on
use in the suspect area could point to samples collected in the index period).
common pesticides, herbicides, or
industrial products or byproducts that
could form the basis of a select list of
contaminants to analyze. Sources for

6.12 Sediment Contaminants
As with water column contaminants,

three approaches to selecting analytes
could be used: (1) a full scan based on
USEPA’s contaminant lists; (2) the
NOAA National Status and Trends suite
of contaminants used by the EMAP
program (refer to Table 3-1); or (3) a
targeted list.
In this latter approach, the historical

information from Tier 0 and subsequent
follow-up inquiries of land use in the
suspect area could point to common
pesticides, herbicides, or industrial
products and byproducts that could
form the basis of a select list of
contaminants to analyze. In addition to
sampling organisms for contaminants,
sediment samples should be collected
from the device used for sampling
benthic infauna. The surface sediment
(top 2-cm) should be removed from
replicate grab samples and composited.
During collection, care should be taken
to avoid collecting material from the
edge of grabs and to use only samples
that have undisturbed sediment
surfaces. The composite sample should
be homogenized, and a subsample taken
for measurement of contaminant
concentrations. Analytical methods are
discussed in APHA (1992) and USEPA
(1992).
Chapter 7
Tier 0: Desktop Screening
large number of sites, and identifying
The breakdown of screening and potentially affected areas for further
sampling in the following chapters that investigation in higher tiers. Table 7-1
focus on the Tiered Approach are just gives an overview of the components,
one way of designing a state-wide sources, and uses of a desktop screening
monitoring program. Agency analysis assessment.
of resources and program objectives
should direct the custom development 7.1 Area and
of any monitoring program. Geomorphometric
Classification
The desktop screening assessment (or
Tier 0) consists of compiling
The size and classification of the estuary
documented information for the estuary
indicates the potential for the
or coastal marine areas of concern
environment to respond to various types
through a literature search and sending
of impacts. In addition, the
survey questionnaires to local experts.
classification refers to the type of
No field observations are made at this
circulation (e.g., gravitational, tidal,
assessment level. Desktop screening
wind-induced) that dominates the
should precede any of the three
estuary. Well-recognized estuary types
subsequent tiers. Its fundamental
include:
purpose is to support the planning for
monitoring and more detailed
< Coastal plain estuary;
assessments. It incorporates time and
< Lagoon;
cost efficiencies, allowing evaluation of a
Table 7-1. Tier 0 Desktop screening for estuaries and coastal marine waters.
Component Information Source Use
Estuary area USGS quad maps, GIS
Geomorphic USGS quad maps, GIS -support planning

classification for monitoring
and more
Habitat type NOAA bathymetry charts; historic surveys by federal, detailed
state agencies, and universities assessments
-incorporates
time & cost
Biological Historic data from federal, state agencies, and efficiencies
assemblages universities. NMFS for marine mammal data -allows evaluation
of a large number
Watershed USGS land use maps; state and county planning of sites
land use agencies; local zoning agencies; USDA CSREES
Population US census data

density
NPDES State water quality agency and regional USEPA offices,

discharges PCS database
Water column Historic data from federal, state agencies, and

& bottom universities; STORET, NODC databases
characteristics
< Fjord; estuary or coastal region, the higher the
< Tectonically-caused estuary. potential for human-induced impacts.
7.2 Habitat Type 7.5 NPDES Discharges
Partitioning of the resource by habitat Industrial and municipal point source

type (open water, soft bottom substrates, dischargers must file monthly discharge
hard bottom substrates, aquatic monitoring reports (DMRs) that provide
macrophytes, high/low energy beaches, the effluent concentrations for the
sandflat, mudflat, emergent marsh) will contaminants in the effluent which they
usually be required and the extent of the are required to monitor. This data is
partitioning will depend on the size of accessible via USEPA’s PCS. Knowing
the system and environmental gradients. the number, type and location of point
Initial subdivisions should be based on source dischargers could provide the
salinity gradients, water depth, and background information necessary for
sediment type, particularly in coastal characterizing the contaminants
marine areas. entering the estuary and the regions
within the estuary or coastline that
7.3 Watershed Land Use would be most affected by the
discharge.
The pollutant and sediment load of fresh
water inflow into the estuary will 7.6 Biological Assemblages
inevitably have some form of impact on
habitat and biota and this land use Existing information on any of the target
information may subsequently help biological assemblages (benthos, fish,
identify causes of impairment. macrophytes, photoplankton,
Nonpoint source pollution has been zooplankton, epibenthos,
shown to be a major contributor to the paleoenvironmental systems) can be
degradation of our aquatic resources. valuable for:
Land use information will help
determine the type of contaminants that < Identifying potential reference sites,
are being flushed into the estuary. For and potentially impaired areas;
example, storm water runoff from
urbanized and industrial areas may < Determining presence/absence of
contain various types of toxins. Runoff major taxonomic groups and
from agricultural areas could be indicator organisms;
expected to contain fertilizers,
pesticides, and sediment. Fertilizers < Evaluating spatial and temporal
have the potential to accelerate variability of the biological
eutrophication by excessive nutrient assemblages.
enrichment, while pesticides may have
at least short-term toxic effects. This information can be used to help
determine target assemblages for
7.4 Population Density higher-level tiers and the sampling
design and methods that might be
This indicates the potential for the appropriate.
whole array of impacts to the estuary
and coastal marine waters from
concentrated human activity. The more
populated the area surrounding the
7-2 Tier 0: Desktop Screening

7.7 Water Column and
Bottom Characteristics
Existing data on water column and

bottom characteristics will be crucial to
support the identification of appropriate
sampling strata based on salinity, grain
size, or depth. Further, this information
can help states identify potentially
impaired areas; i.e., areas receiving high
nutrient loadings or containing
contaminated sediments.
Chapter 8
Tier 1
The Tier 1 assessment is just one way of < detection of potential impairment of
completing a minimal biological benthic macroinvertebrate and fish
assessment or simple field screening. assemblages;
Specific agency needs will ultimately
decide the components of any state < detection of oxygen stress.
monitoring program. The time period of
sampling should be selected to allow The Tier 1 assessment will not allow
states to answer the question: “What separation of multiple probable causes.
information do we want to obtain from a It can establish the initial habitat
single site visit?” For example, it could classification scheme and identify
be conducted from a single field visit several possible causes of impairment,
during late summer when low dissolved including point sources, nearfield
oxygen concentration, due to nonpoint sources (in the immediate
stratification and eutrophication, is most shore zone of the coast or estuary), and
likely to occur or during some other farfield nonpoint sources (from land use
chosen index period, depending on the in the drainage). It cannot, however,
monitoring purpose. It builds on the identify the most probable from among
information compiled in the desktop several possible causes. It should also
screening assessment and consists of help establish the most likely sites to use
sampling one or more biological in developing the reference condition
assemblages and collecting data on and test their candidacy for this
water column and bottom characteristics preliminary phase of biocriteria
(Chapters 5 and 6). Tier 1 might roughly development. Table 8-1 gives an
identify whether an estuary or coastal overview of the components, data
marine waters are nutrient enriched and collection methods, and indicators for
can distinguish among broad probable Tier 1.
causes if the nutrient state is different
from expectations (reference conditions). 8.1 Benthos
This assessment tier enables:
Sampling and analysis of benthic
< coarse identification of nutrient state infaunal macroinvertebrates in Tier 1 is
based on chlorophyll a intended to provide a rapidly obtained
concentration, and identification of snapshot of the condition of the benthic
point and nonpoint probable cause if assemblage. It is recognized that this
stations are carefully selected and assemblage, and the methods presented,
spaced; will be most appropriate for sites with
soft sediments (e.g., mud, silt, sand).
< detection of emergent wetlands and For sites with hard bottom substrates,
shore zone fish habitat loss from other biological assemblages (e.g., fish,
shore zone survey and macrophyte macrophytes, phytoplankton) could be
assessment; selected to provide information on the
biological condition of the target waters.
< detection of loss of submerged
aquatic macrophytes; The sampling strategy presented here
consists of collecting replicate grab
Table 8-1. Tier 1 Assessment. Requires single field visit in spring or summer index period.
Component Data Collection Indicator of Uses
*3 replicate grabs DO stress, toxicity, -Identification of

Benthic Infauna
*x-section of Smith-McIntyre or low productivity, nutrient state
Young grab nutrient based on
*measure RPD depth enrichment, habitat chlorophyll a
*brief description of classes & impairment concentration &
families of benthos present in grab identification of
*record faunal presence/absence point and nonpoint
of benthos above and below the probable causes (if
RPD depth in sediment x- section stations are
carefully selected
*3 trawls DO stress, toxicity, & spaced)
*3 seines habitat impairment -Detection of
Fish
*species counts emergent wetland

*measure standard lengths & shorezone fish
*record external abnormalities habitat loss from
shorezone survey
and macrophyte
Phytoplankton Macrophytes
*aerial photos (if possible - or Nutrient

estimate from shorezone survey enrichment, assessment
*% cover estimate sediment loading -Detection of loss
*record dominant taxa of submerged
aquatic
macrophytes
*chlorophyll a Nutrient
*record blooms enrichment
*identify dominant species
Water Column Characteristics
*salinity/conductivity DO stresses, -Detection of

*temperature eutrophication, potential
*DO stratification, impairment of
*pH turbidity benthic
*Secchi depth macroinvertebrate
*depth & fish
*TSS for seagrass assemblages
*grain size estimate & description Habitat -Detection of

*RPD layer depth modification, DO oxygen stress
*TVS stress, sediment
*sediment toxicity toxicants
samples at each sampling site, taking a may also wish to sort and identify the
vertical cross-section of the sample, and organisms found above and below the
measuring the RPD layer depth to RPD depth for additional information
record the presence/absence of benthos relative to Tier 2. The method presented
above and below the RPD depth in the here is a simplification of the Benthic
sediment cross-section. In addition to Assessment Method developed by Diaz
the actual presence of organisms, and Nelson (1993). Functional attributes
evidence of their presence, such as of the benthic infaunal community that
bivalve siphons, siphon impressions in can be evaluated using these procedures
clay/mud, or polychaete burrows, include:
should also be noted. The investigator
8-2 Tier 1
< Species Life Histories The presence of A sieve with mesh size appropriate for
relatively large and long-lived the region should be used. The presence
species, especially those found or absence of benthic infauna in either
deeper in the sediments, indicate subsample is noted. If present, the
higher quality habitat than does the classes and families should be noted and
presence of small and short-lived recorded.
taxa;
8.1.2 Index Period
< Major Taxa Abundance High
abundance of only a few taxa, Benthic infaunal macroinvertebrates are
usually pollution tolerant ones, sampled once during an appropriate
indicates a degraded environment; index period, the timing of which is
driven by the goals of the Tier 1
< Major Taxa Biomass Distribution assessment and regional considerations.
Larger organisms, hence a higher
biomass per individual, are more 8.1.3 Analysis
prevalent in better quality habitats;
Note the presence/absence of an RPD
< Vertical Distribution of Biomass layer and any infauna (or evidence of
Organisms living below 5-cm in soft infauna) below 5-cm depth in the
substrates indicate a relatively high sample. If present, identify benthic
quality habitat. infauna to class and family and record
abundance.
8.1.1 Sampling Procedure
8.2 Fish
The primary objective of benthic
infaunal macroinvertebrate sampling in A Tier 1 assessment of the fish
Tier 1 is to determine whether there are assemblage is intended to provide a
any large organisms below the RPD rapid evaluation of its presence and
depth. The recommended sediment overall composition. Fish sampling in
sampling procedure involves collecting Tier 1 can include shallow-water,
three replicate grab samples at each pelagic, and demersal fish communities
station using a Smith-McIntyre or Young (Carmichael et al. 1992, Eaton and
grab. The selection of sampling gear Dinnel 1994, Guillen 1995a).
should be made to maximize
compatibility with historic data. For 8.2.1 Sampling Procedure
example, the state of Texas uses an
Ekman grab, and has an approximately Various nets can be used to sample
25-year data record using this gear type. littoral and sublittoral areas. It is
The sediment sample is vertically recommended that trap nets (gill or fyke
bisected using a sheet metal partition. nets) be set and fished twice a day for 2-
The RPD layer depth is noted and to 5-days. Due to the risk of boating
measured, if present, as the distance mishaps and vandalism, it is
from the sediment surface to a recommended that investigators stay
noticeable change in color from with the nets while they are being
brownish (oxidizing conditions) to gray fished. Fish sampling methods are
(reducing conditions). The sediment detailed in Klemm et al. (1992).
above the RPD depth is removed and
wet-sieved separately; the remaining < Gillnets are set in littoral areas at
portion of the sample is also wet-sieved. right angles to the shore or to
longshore fish movement. Gillnets small matter of convenience, both scales
usually extend into sublittoral areas. should weigh in metric units. Those
Smaller mesh size (0.5") is used in animals not saved for further
shallow areas and up to 2 to 2.5"
mesh is used further away from examination should be promptly
shore. To reduce size selectivity, an returned to the water.
experimental gillnet consisting of
panels of five different mesh sizes is The investigator should consult with
commonly used; State and University fish pathologists of
the region for those most appropriate
< Trawl nets and sonar can be used to sample preparation and preservation
sample pelagic and demersal areas. techniques. Usually iced or frozen
The length of the towline (warp) specimens are inappropriate and in
should be at least six times the depth some cases formaldehyde or other tissue
of water and a trawl speed of about preservatives must be carefully used if
2-knots over a 0.5-nautical mile meaningful samples are to be presented.
distance is appropriate for coastal Generally, small fish can be tagged and
marine waters. These values of placed whole in 10% formalin. Larger
warp length and trawling distance fish will require dissection in the field
can be reduced in estuaries. A 20-ft and the tissue samples tagged and
trawl (16-ft effective trawl mouth) is preserved in the same manner.
appropriate in marine waters, but an Protocols for preservation and dissection
8- or 10-ft trawl is easier to tow in should be obtained from the
restricted waters. laboratory/fish pathologist that will
receive the samples.
8.2.2 Sample Processing
When collected, reference specimens of
Sampling duration and area or distance each species from each site are
sampled (from DGPS) are recorded in preserved in 10% formalin in a labeled
order to determine sampling effort. jar and retained by the state
Species are identified and enumerated. ichthyological museum or other
Fish should be carefully removed from designated repository to constitute a
the net to avoid undue handling and biological record. This is especially
damage. The catch should be sorted by important for uncommon species, for
species, and length measurements made species requiring laboratory
of each individual. This measurement is identification, and for documenting new
usually total length, but fork length or distribution records. Later, all
standard length can also be used. At the specimens should be transferred from
time of measurement, any deformities, formalin to 70% alcohol for long-term
ulcerations, bleeding, fin rot, bulging storage.
eyes or other disease indicators should
be noted and those fish saved for 8.3 Macrophytes
histopathology. It is important to
distinguish net damage from pre- Areal coverage and distribution of
existing conditions, if possible. Wet submerged aquatic macrophytes is
weights can be taken by species by estimated from aerial photographs, if
weighing the fish either individually available, and ground-truthed at the site.
using a platform scale or collectively The dominant taxa may be field-
from tared hanging scales, depending identified from vegetation samples
on the number of fish caught. As a collected in shallow waters. Detailed
8-4 Tier 1
macrophyte monitoring and assessment
procedures are included in USEPA
(1992), Ferguson and Wood (1994), and
Orth et al. (1993).
8.4 Phytoplankton
Phytoplankton standing stock is

estimated by chlorophyll a
measurements. A sample is collected at
each station at one-half the Secchi depth
using a Kemmerer or Van Dorn sampler.
Chlorophyll a is determined using a
fluorometer or spectrophotometer as
discussed in APHA (1992). The
presence of any phytoplankton blooms
observed during the cruise should be
noted. Dominant phytoplankton species
should be identified.
Chapter 9
Tier 2
Tier 2 assessment is considered a routine < Identification of phytoplankton taxa

biological survey that incorporates two responsible for blooms.
or more field visits per year to capture
variations due to seasonal differences. A Tier 2 assessment should allow
Tier 2 comprises increased sampling identification of multiple probable
effort and additional assemblages causes of impairment, given an adequate
compared to Tier 1. It includes two or number and placement of sampling
more biological assemblages (benthos, stations. This includes point sources,
fish, macrophytes, phytoplankton, or and nearfield and farfield nonpoint
epibenthos), in 2 or more visits per year, sources. Preliminary management plans
in addition to more detailed in response to the biocriteria
characterization of the water column information can be developed. Table 9-1
and bottom (Chapter 5). State agencies gives an overview of the components,
can modify this schedule to data collection, methods, and indicators
accommodate their program objectives. for Tier 2.
This level is sufficient for identification 9.1 Benthos

of appropriate habitat classes and
determination of the reference condition Sampling and analysis of benthic
for development of biological criteria. infauna in Tier 2 is intended to provide a
Data collected in Tier 2, which level of assessment consistent with
incorporates both Tier 1 and Tier 0, routine benthic macroinvertebrate
should permit the state to confidently surveys presently conducted by states in
develop biocriteria and apply them to estuaries and coastal marine waters. As
identify problem areas. This assessment with Tier 1, this assemblage, and the
level enables: methods presented, will be most
appropriate for soft sediments. For sites
< Establishment of the biocriteria with hard bottom substrates, other
“benchmarks” for decision-making biological assemblages (e.g., fish,
about impaired areas; including macrophytes, phytoplankton) could be
identification of priorities; selected to provide information on the
biological condition of the target waters.
< Identification of trophic state based
on chlorophyll a and water column The sampling strategy for Tier 2 entails a
nutrient measurements; minimum of two field collection visits,
one of which should occur within the
< Detection of impairment of benthic chosen index period. Organisms are
macroinvertebrate, fish, or identified to genus and species to
epibenthos assemblages, and determine major taxa and the presence
evaluation of potential causes of the of indicator organisms. Water column
impairment; and bottom characteristics are also
measured to evaluate the status of
< Measurement of extent of physicochemical conditions.
macrophyte coverage;
Table 9-1. Tier 2 Assessment. Requires two or more field visits, one of which should occur within
chosen index period. In addition to requirements from Tiers 0 & 1.
*3 replicate grabs (or as -Establishment of biocriteria

determined by testing; see “benchmarks” for decision-
Infauna
Benthic
Section 5.2.6 making about impaired

*identify major taxa and indicator areas, including
spp. of each grab to genus and identification of priorities
species -Identification of trophic
state based on chlorophyll
*3 or more replicates a and water column nutrient
Fish
*biomass by species measurements

-Detection of impairment of
benthic macroinvertebrate,
*area Habitat fish, or epibenthos

*maximum depth impairment assemblages and
*identify taxa and measure wet evaluation of potential
weight of 2-3 samples per causes of impairment
transect -Measurement of extent of
macrophyte coverage
*identify dominant species, -Identification of
including “nuisance” taxa, on a phytoplankton taxa
seasonal basis responsible for blooms
(developmental)
*mid-summer or growing season

average at genus and species
Epibenthos
level
*calculate sensitivity metric
*nutrients: NH4, NO3,NO2,

Kjeldahl N, total and reactive P
*grain size measurements Organic

*TOC enrichment
9.1.1 Sampling Procedure procedure involves collecting three

replicate grab samples at each station
Primary objectives of Tier 2 benthic using a Smith-McIntyre or Young grab.
infaunal sampling are to evaluate Sampling gear should be selected to
potential impairment to this assemblage maximize compatibility with historic
and to generate the data necessary to data. The sediment sample is vertically
develop biocriteria. This Tier, unlike bisected using a sheet metal partition.
Tier 1, incorporates multiple sampling The RPD layer depth is noted and
visits to allow a basic discrimination of measured, if present, as the distance
seasonal differences in the benthic from the sediment surface to a
infaunal macroinvertebrate assemblage. noticeable change in color from
The recommended sediment sampling brownish (oxidizing conditions) to gray
9-2 Tier 2
or black (reducing conditions). The condition of the macroinvertebrate
sample should be wet sieved through a assemblage is evaluated.
sieve mesh size determined to be
appropriate for the region (Section 6.3.2). 9.2 Fish
For cost and effort savings, an
appropriate diameter subcore (2.5- or 5- Tier 2 assessment of the fish assemblage
cm) can be taken from each of the four is intended to provide data sufficient to
quadrants of the intact core. These evaluate impairment and to develop
subcores should be compared to biocriteria. Fish sampling in Tier 2 can
organism counts taken from full cores to include shallow water, pelagic, and
establish the baseline relationship demersal fish communities (Carmichael
between the two. Organisms and et al. 1992, Eaton and Dinnell 1994,
sediment fractions should be placed in Guillen 1994).
tagged and labeled sample jars with a
10% solution of magnesium chloride or 9.2.1 Sampling Procedure
magnesium sulfate to narcotize the
animals. After at least 30-minutes, See Section 8.2.1 for full procedure on
concentrated formaldehyde with rose sampling fish.
bengal dye can be added to the jars to
make a 10% solution of formaldehyde 9.2.2 Sample Processing
by volume. The sediment/organism
material should never exceed half the See Section 8.2.2 for full procedure on
container volume to ensure adequate sample processing.
mixing and fixation of the sample. For
preservation, the samples should be 9.2.3 Analysis
transferred to 70% ethanol (APHA
1992). Based on the enumerated species list,
metrics selected by the state can be
9.1.2 Index Period calculated to evaluate potential
impairment to the fish assemblage and
Benthic infaunal macroinvertebrates are to develop biocriteria for this
sampled once during an appropriate assemblage.
index period, the timing of which is
driven by the goals of the Tier 2 9.3 Macrophytes
assessment and regional considerations.
At least one other sampling visit is made Tier 2 assessment of macrophytes is
outside the index period to capture basic intended to provide sufficient data to
seasonal differences in the assemblages. assess impairment to the macrophyte
The timing of this visit(s) will depend on assemblage as a significant habitat
the specific goals of the assessment. variable and potential element of
biocriteria. Because of its importance as
9.1.3 Analysis habitat for other assemblages,
procedures for Tier 2 assessment of
Organisms in each sample are identified macrophytes are considerably more
to genus and species. Metrics selected involved than for Tier 1.
by the state can then be calculated to
assess the condition of the assemblage. 9.3.1 Sampling Procedure
Metric values can then be used to help
develop biocriteria against which the The extent of coverage and distribution
of macrophytes should be determined
from aerial photographs. Existing aerial diminishment of important nursery or
photographs are inexpensive; however, food areas.
they may not be sufficiently recent to
depict present macrophyte distribution 9.3.3 Analysis
in the water body. If new aerial
photographs are determined to be Percent cover and area may be derived
needed, states should recognize that from analysis of aerial photographs.
overflights can be expensive and The maximum depth of occurrence is a
complicated; often requiring assistance good indicator of water quality.
from firms specializing in aerial Taxonomic identification from the field
photography. Factors to consider when trips will allow development of a species
planning new overflights include: tidal list.
stage; weather conditions; time of day;
and water turbidity (USEPA 1992). 9.4 Phytoplankton
Ferguson and Wood (1994) and Orth et
al. (1993) describe details of planning 9.4.1 Sampling Procedure
aerial overflights, obtaining imagery,
photointerpretation, and preparation of Phytoplankton standing stock is
macrophyte distribution maps. estimated by chlorophyll a
measurements. One approach might be
A key aspect of interpreting aerial three replicate samples collected at each
photographs is the performance of station at one-half the Secchi depth
ground surveys that serve to confirm the using a Kemmerer or Van Dorn sampler.
existence of macrophyte beds identified Another approach would collect a
in the photographs, as well as beds that depth-integrated sample through the
may not be visible in the photos (Orth et entire photic portion of the water
al. 1993). Transects can be plotted across column. Chlorophyll a is determined
macrophyte beds in the various salinity using a fluorometer or
zones within an estuary or within the spectrophotometer as discussed in
sampling strata used for marine waters. APHA (1992). The presence of any
At each station on the transect a 1-m2 phytoplankton blooms should be noted.
quadrat can be used for the purpose of In addition to chlorophyll a
measuring percent cover and collecting measurements, samples from each
macrophyte samples for taxonomic station should be preserved for
identification and measurement of wet subsequent analysis to identify the
weight (USEPA 1992). Depth at the dominant taxa and those taxa that might
channel-ward or seaward edge of be responsible for observed blooms
macrophyte extent should be recorded. (USEPA 1992).
9.3.2 Index Period 9.4.2 Index Period
Aquatic macrophytes should be Phytoplankton populations can vary

sampled once during an appropriate rapidly over space in response to tides
index period, preferably during the time and currents, and over time in response
of year when they would be expected to to ambient temperature and nutrient
be most dense and extensive. Other inputs. For Tier 2, phytoplankton
sampling periods should be selected should be sampled at least once during
based on the specific goals of the Tier 2 an index period (usually summer) and at
assessment, perhaps to measure least once outside that index period.
seasonal periods of stress or
9-4 Tier 2
9.4.3 Analysis effectively sampling 5-m2 of bottom) in
estuaries may be beneficial for reducing
Chlorophyll a measurements can be the sample size and detrital bulk. If a D-
used to estimate phytoplankton frame net is used, at least an equivalent
standing stock. Assuming that area should be sampled. In offshore
chlorophyll a is about 1.5% of the ash- waters, it may be necessary to increase
free dry weight of algae, algae biomass the tow length due to reduced organism
can be estimated by multiplying the densities. Small otter trawls or an
chlorophyll a content by a factor of 67 epibenthic sled sampler can also be
(APHA 1992). This information can be used.
used in concert with the identification of
dominant taxa and “nuisance” taxa to 9.5.2 Index Period
assess the overall condition of the
phytoplankton assemblage. Epibenthos should be sampled once,
preferably during an appropriate index
9.5 Epibenthos period. For many temperate areas of the
country, this is probably mid-summer.
(Developmental)
Other sampling periods should be
Although its use as an indicator of selected based on the specific goal of the
estuarine and coastal marine biological Tier 2 assessment.
condition is considered to be under
development, epibenthos could be 9.5.3 Analysis
selected as one of the biological
assemblages for a Tier 2 assessment and The samples should be identified to
has potential as an element of biological genus and species. The Farrell Index
criteria consistent with fish and benthic (described in Chapter 13 - Case Studies,
invertebrates. as modified to reflect tolerance values of
taxa in the area sampled) should be
calculated to provide an assessment of
9.5.1 Sampling Procedure
the condition of the assemblage in
Farrell (1993a, b) describes the use of a response to organic pollutants and
beam trawl to collect epibenthos. A eutrophication. Other metrics could be
beam trawl is a conical-shaped net, open calculated based on the specific taxa
at the large end, which is towed over the present.
substrate surface. The net is kept open
by attaching each end of it to a rigid pole
or beam. This beam replaces the doors
of an otter trawl and forward movement
of the boat is not required to keep the
net open. The net is constructed in two
parts. The body is nylon bolting cloth
(50 openings/cm2 ), tapering to a
plankton net fitted with a removable
container. An effective swath width of
1.25-m has been tested in Florida waters
(Farrell 1993a, b). In wadeable water, a
D-frame net could be used to collect
epibenthos, or the beam trawl could be
pulled by hand. A relatively short tow
length of the beam trawl (4-m,
Chapter 10
Tier 3
Tier 3 is the most rigorous of the < Detection of impairment of benthos,

assessment tiers. It includes more fish, macrophytes, phytoplankton,
detailed assessment procedures that zooplankton, epibenthos, or
allow monitoring agencies to focus on paleoenvironmental systems;
specific water and sediment quality
problems in estuarine or coastal marine < Diagnosis of specific sources and
waters. Tier 3 is intended to provide causes of impairment;
definitive information needed to act on
biocriteria and to measure potential < Measurement of extent of
success or failure of the management macrophyte coverage;
effort. It allows states to conduct a
detailed diagnosis of the sources and < Identification of phytoplankton taxa
causes of impairment to biological responsible for blooms;
assemblages and the physicochemical
environment and to monitor their < Evaluation of seasonal dynamics of
response to subsequent mitigation biological assemblages;
actions. However, the Tier 3 approach
can be customized to accommodate < Detailed monitoring of sites
specific state program objectives. Table requiring management initiatives to
10-1 gives an overview of the meet the biocriteria;
components, data collection methods,
and indicators for Tier 3. < Inferences of past conditions as a
site-specific reference.
Tier 3 assessments include multiple
sampling visits per year (four or more) 10.1 Benthos
that occur within each season including
the index period. Data collected in Tier Sampling and analysis of benthic
3, which includes information compiled infaunal macroinvertebrates in Tier 3 is
in Tier 0 desktop screening and intended to provide a diagnostic level of
comprises the information collected in assessment. This assemblage, and the
Tiers 1 and 2, involves sampling and methods presented, will be most
measurement of three or more biological appropriate for soft sediment. For sites
assemblages (benthos, fish macrophytes, with hard bottom substrates, other
phytoplankton, zooplankton, or biological assemblages (e.g., fish,
epibenthos), in addition to more detailed macrophytes, phytoplankton,
characterization of the water column zooplankton) could be selected to
and bottom. A Tier 3 assessment provide information on the biological
enables: condition of the target waters.
< Identification of nutrient state based The sampling strategy for Tier 3 entails a
on chlorophyll a and water column minimum of four field collection visits
nutrient measurements; per year, one of which should occur
within the chosen index period. The
remaining visits should occur
throughout the year to allow evaluation
Table 10-1. Tier 3 Assessment. Requires four or more field visits, one of which should occur within the
chosen index period. In addition to requirements from Tiers 0-2.
Infauna
Benthic *determine biomass -Identification of nutrient state
*calculate multiple based on chlorophyll a & water
metrics column nutrient measurements
-Detection of impairment of
*5 or more replicates Fishing benthos, fish, macrophytes,
phytoplankton, zooplankton,
Fish
*histopathology on pressure, epibenthos, or paleoenvironmental

representative disease systems
subsample of catch -Diagnosis of specific sources &
causes of impairment
*stem counts Toxicity, habitat -Measurement of extent of

*biomass impairment, macrophyte coverage
*record pathology disease -Identification of phytoplankton
taxa responsible for blooms
-Evaluation of seasonal dynamics
of biological assemblages
-Detailed monitoring of sites
*full community requiring management initiatives
characterization to to meet the biocriteria
species -Integrate conditions over broad
spatial scales
(developmental) (developmental) Systems (developmental)
*2 or 3 cores from Past conditions

basin (one-time
sample)
Paleoenvironmental
See Tier 2
Epibenthos
*identify to species Water quality

impairment, DO
Zooplankton
stress
*pesticides, herbicides pesticides/

*metals herbicides,
metals
*AVS
*sediment
contaminants
(organics, metals)
10-2 Tier 3
of seasonal differences in the benthic ash-free dry weight, at least to the
macroinvertebrate assemblages. family level, may be measured to
Organisms are identified to genus and determine the viability of biomass-
species. Water column and bottom based metrics to the overall
characteristics are also measured to assessment. Other metrics should be
evaluate the status of physicochemical selected by the resource management
conditions. agency as appropriate based on
historic data, data collected and
10.1.1 Sampling Procedure metrics used in preceding tiers, and
regional considerations.
Primary objectives of Tier 3 benthic
infaunal sampling are to evaluate 10.2 Fish
potential impairment to this
assemblage, to develop and refine Tier 3 assessment of the fish
biocriteria, to diagnose causes and assemblage is intended to allow
sources of observed impairment, and evaluation of impairment, to develop
to evaluate seasonal changes in the and refine biocriteria, to diagnose
benthic infauna. This tier includes causes and sources of impairment,
more frequent sampling (a minimum and to evaluate seasonal differences in
of four times per year) than either the assemblage. Fish sampling in this
Tiers 1 or 2 to allow detailed tier can include shallow-water,
discrimination of seasonality of pelagic, and demersal fish
benthic abundance. See Section 8.1.1 communities (Carmichael et al. 1992,
for full detail on sampling procedures. Eaton and Dinnell 1994, Guillen 1994).
10.1.2 Index Period 10.2.1 Sampling Procedure
Benthic infaunal macroinvertebrates See Section 8.2.1 for full description of

are sampled once or twice during an fish sampling procedures.
appropriate index period, the timing
of which is driven by the goals of the 10.2.2 Sample Processing
Tier 3 assessment and regional
considerations. At least two or three See Section 8.2.2 for full description of
other sampling visits are made fish sample processing.
throughout the remaining portion of
the year to capture more detailed 10.2.3 Analysis
seasonal differences in benthos than
would be possible in a Tier 2 Based on the enumerated species list,
assessment. Data collected in a metrics selected by the state can be
previous Tier 2 assessment, or historic calculated to evaluate potential
benthic infaunal macroinvertebrate impairment to the fish assemblage, to
data, can be used to determine the develop or refine biocriteria, to
timing and frequency of non-index examine seasonal dynamics of the
period sampling. assemblage, or to diagnose sources
and causes of impairment.
10.1.3 Analysis
10.3 Macrophytes
Organisms in each sample are
identified to genus and species. If Tier 3 assessment of macrophytes is
desired, and resources are available, intended to provide sufficient data to
assess impairment to the macrophyte the assessment tiers described here,
assemblage, to develop or refine the resource management agency may
biocriteria, or to diagnose sources and determine that a higher frequency of
causes of impairment. sampling is needed to characterize the
phytoplankton assemblage based on
10.3.1 Sampling Procedure its potential for rapid spatial and
temporal variation.
See Section 8.3.1 for full description of
macrophyte sampling procedures. 10.4.3 Analysis
10.3.2 Index Period See Section 9.4.3 for a full description

of phytoplankton analysis.
See Section 8.3.2 for full description of
the macrophyte index period. 10.5 Epibenthos
(Developmental)
10.3.3 Analysis
As in Tier 2, even though epibenthos
Percent cover and area may be is currently under development as a
derived from analysis of aerial biological indicator, it can still be
photographs. Taxonomic useful in the Tier 3 assessment.
identification from the field trips will
allow development of a species list. 10.5.1 Sampling Procedure
Stem counts made within quadrats
along each sampling transect in See Section 9.5.1 for a full description
addition to biomass determination of the epibenthos sampling procedure.
will provide more detailed
information on assemblage condition. 10.5.2 Index Period
Detailed pathology observations
should be made; they can be used to See Section 9.5.2 for a full description
evaluate potential causes of of the epibenthos index period.
impairment.
10.5.3 Analysis
10.4 Phytoplankton
See Section 9.5.3 for a full description
10.4.1 Sampling Procedure of epibenthos analysis.
See Section 9.4.1 for a full description 10.6 Zooplankton

of the phytoplankton sampling
(Developmental)
procedure.
Zooplankton are an important link
10.4.2 Index Period between phytoplankton in estuaries
and coastal marine waters and higher
Phytoplankton should be sampled at
consumers. States might choose to
least once during an appropriate
include this developmental
index period and a minimum of three
assemblage as part of a Tier 3
other times per year to capture
assessment.
seasonal changes in the composition
and abundance of the assemblage.
Following review of data collected
from historical data or through any of
10-4 Tier 3
10.6.1 Sampling Procedure By comparing past biota with present-
day biota, past environmental
Three replicate vertical tows using a conditions can be inferred. Several
118-:m mesh net, 30-cm in diameter groups of organisms have been used:
should be made at each sampling diatoms, foraminifera, and
location. The tow should be vertically dinoflagellate cysts. Of these, diatom
integrated; that is, starting from 0.5-m frustules and foraminifera have been
from the bottom to the surface, with a used most often, and most
retrieval rate of 0.5- to 1-ms-1 . successfully, to infer past conditions.
Collected organisms should be A sample of the top 1- to 2-cm of
anesthetized with carbonated water sediment contains a representative
and preserved in 4% formalin. For sample of diatoms from the most
long-term storage after fixing, recent 1- to 5-years. If the sediments
specimens should be transferred to remain undisturbed, then remains
70% ethanol. APHA (1992) describes preserved in the sediments are
procedures for concentrating the integrators of estuarine history
samples and preparing them for (Charles et al. 1994, Dixit et al. 1992).
examination. Because of the developmental nature
of this indicator, states or agencies
10.6.2 Index Period wishing to use paleoenvironmental
reconstruction should contact one of
Zooplankton should be sampled once the laboratories engaged in this
during an appropriate index period research for further information. The
and a minimum of three other times methods described here are intended
during the year to capture seasonal to give a brief overview of the field,
variation in taxonomic composition but should not be used to plan a
and abundance. monitoring program.
10.6.3 Analysis 10.7.1 Sampling Procedure
Samples should be identified to the Cores are generally taken with

lowest practical taxonomic level, standard gravity corers, such as the K-
preferably genus and species. B, Phleger, or Piston. The chosen
Subsampling may be required to corer should retrieve a core deep
achieve reasonable numbers of enough to sample sediments from the
organisms for identification. earliest desired time period, with
minimal edge disturbance. Core
10.7 Paleoenvironmental length thus depends on time period
and sedimentation rate. Core samples
Systems
are extruded from the corer and
(Developmental) subsectioned immediately after
collection. Sections 1-cm thick are
Developmental assessment of
removed from the core at intervals
paleoenvironmental systems is
according to the time resolution
intended to provide site-specific
desired. These sections are removed
reference by showing past conditions.
from the core using an apparatus
Several groups of organisms leave
described by Glew (1988) then are
remains in the bottom sediments.
bagged, labeled and identified using a
Some of the remains are resistant to
permanent ink pen. The bags
decay and become a permanent
prepared from a single core sample
biological record of life in the estuary.
are placed in a sealed container for al. 1999, Alve 1991). Additional time
storage and transport. Samples are points can be established from traces
kept at 4°C until shipment. of known historic events (charcoal
from large-scale fires, radioisotopes
10.7.2 Sample Processing from atmospheric testing and the
Chernobyl accident). Known
Once in the laboratory, the sections responses of indicator taxa or
are dried and weighed. Foraminifera biogeochemical indicators (e.g.,
and diatoms are processed so as to biogenic silica) are used to infer past
digest organic matter and preserve environmental conditions of an
carbonate (foraminifera) or silica estuary. This allows for the
(diatoms), following the standard assessment of current environmental
methods of Krom and Berner (1983) conditions based on those of the past.
and EMAP (USEPA 1994e). An
aliquot of frustules or tests is mounted Quantitative paleoenvironmental
for optical and/or scanning electron reconstruction in estuaries requires
microscopy for identification. the development of a data set that
Dinoflagellate cysts are subjected to a associates current conditions with
standard pollen analysis involving the current surficial diatom,
digestion of minerals in cold HCl, dinoflagellate, or foraminifera
followed by warm HF (adapted from assemblages. Present-day associations
Barss and Williams 1973). They are are used to infer past conditions based
processed on a 10 :m sieve. Samples on fossil assemblages in deeper
for counting and identification are not sediment layers. Quantitative
random, but systematic. prediction is usually done in two
steps: development of predictive
Transects are taken on microscope models (calibration or transfer
slides, counting and identifying all functions), followed by use of the
target taxa encountered. A count of models to infer environmental
300 or more is necessary for variables from fossil assemblages
meaningful analysis of percentage (Charles and Smol 1994). Quantitative
data, but lower counts are still valid if reconstruction has not yet been widely
results are reported on a concentration developed for estuaries.
basis. In some depositional systems it
is not feasible to count 300
dinoflagellate cysts, but the data is
still informative.
Charcoal is seen in pollen analysis and

dinoflagellate cyst preparations. The
larger sieve size used for foraminifera
would exclude most charcoal
particles, thus make this material
unsuitable for charcoal studies.
10.7.3 Analysis
Standard dating methods use either

carbon-14, pollen, 137 Cs, or 210 Pb (Dixit
1992, Cooper and Brush 1991, Dale et
10-6 Tier 3
Chapter 11
Index Development
11.1 Overview the Virginian and Louisianan provinces

(Weisberg et al. 1993; Schimmel et al.
Many methods have been developed to 1994; Strobel et al. 1994; Summers et al.
assess the condition of water resources 1993, 1994; Engle et al. 1994). The
from biological data, beginning with the EMAP-NC, Louisianian and Virginian
saprobien system in the early 20th Province examples will be used to
century to present-day development of illustrate the method.
biological markers. This chapter will
discuss three methods for analyzing and 3. Index derived from multivariate
assessing water body condition from ordination.
assemblage and community-level
biological information: Smith et al. (2000) and Allen and Smith
(2000) have developed a pollution
1. Multimetric index. tolerance index for near-coastal sites of
Southern California, using species
This is the basis of many indexes used in composition of benthic
fresh waters: the Index of Biotic macroinvertebrates and demersal fish.
Integrity (IBI; Karr et al. 1986), the Other approaches using ordination have
Invertebrate Community Index (ICI; demonstrated differences in
Ohio EPA 1987); the Rapid composition between reference and
Bioassessment Protocols for Use in stressed sites (e.g., Warwick and Clarke
Wadeable Streams and Rivers: 1991). The approach of Smith et al. uses
Periphyton, Benthic Macroinvertebrates, ordination of species composition to
and Fish, Second Edition (RBP; Barbour develop a numeric index on a scale of 0-
et al. 1999); and state indexes developed 100, that can be used directly for
from these (e.g., Southerland and biocriteria. The Smith et al. example
Stribling 1995). More recently, will be used to illustrate the method.
multimetric IBI - type indexes have been
developed for estuarine assemblages Many other methods are possible, as
(e.g. Cape Cod fish, Deegan et al. 1997; well as permutations of the three
Chesapeake Bay macroinvertebrates, methods above, all of which are beyond
Weisberg et al. 1997; Carolinian the scope of this document. These three
Province macroinvertebrates, Hyland et were selected because:
al. 1998). The Chesapeake Bay
development (Weisberg et al. 1997) will < They use community and
be used to illustrate the method. assemblage data;
2. Discriminant model index. < The methods are not restricted to

any one assemblage. The examples
This is the basis of stream bioassessment all use benthic macroinvertebrates,
in Maine (Davies et al. 1993), and of the but any other assemblage could also
estuarine invertebrate indexes be used, such as fish,
developed by the EMAP-NC program in
phytoplankton, zooplankton or 11.2 Classification and
macrophytes; Characterization of
Reference Condition
< The examples used to illustrate the
methods have been carried out over
The objective of characterization is to
wide geographic areas with many
finalize the classification of reference
sites, demonstrating the generality of
sites and to describe (characterize) each
the methods;
of the reference classes in terms of
metrics, assemblage composition, and
< The examples used to illustrate the
physical-chemical variables. As
methods are concise, the methods
outlined in Chapter 4, classification may
were fully documented, and have
be a physical rule-based classification,
been carried to completion, that is,
or an analytical data interpretation
assessment of biological impairment
where rules are derived from the data.
and non-impairment.
The analytical approach requires a
relatively large reference data set to
All three of the methods use the same
derive the classes and rules, with many
general approach: sites are assessed by
sites and both biological and
comparing the assemblage of organisms
physical-chemical data from each site.
found at a site to an expectation derived
from observations of many relatively
The basic assumption of classification is
undisturbed reference sites. The
that biogeography, physical habitat, and
expectations are modified by classifying
water quality largely determine
the reference sites to account for natural
attributes such as taxa richness,
variability, and each assessment site is
abundance, and species dominance in
classified using non-biological (physical,
estuarine and coastal marine biological
chemical, geographic) information.
communities. In other words, if
Finally, metrics (methods 1 and 2) or the
habitats are classified adequately,
species ordination (method 3) are tested
reference biological communities should
for response to stressors by comparison
correspond to the habitat classification.
of reference and known impaired sites.
An example of the assessment process is
Several statistical tools can assist in site
summarized in Figure 11-1.
classification, but there is no one set
procedure. If the rule-based
This chapter will first discuss methods
classification is based on well-
of classification, with emphasis on those
developed prior knowledge and
that have been successful in estuaries
professional judgment, graphical
and coastal waters. The remainder of
analysis of metrics, followed by any
the chapter then discusses the three
necessary modifications and tests of the
assessment methods. This chapter is not
resultant classification, it is usually
intended to be an instruction manual on
sufficient. If necessary, the classification
using the different statistical methods; it
is refined until an optimal classification
is intended to show, with selected
emerges that satisfactorily accounts for
examples, techniques that have been
variation in reference site biological
used to develop biological indexes.
data.
Details of applications and methodology
can be found in the cited documents and
If a physical classification is not self-
articles and in statistical textbooks and
evident, it may be necessary to develop
manuals (e.g., Ludwig and Reynolds
an alternative classification from the
1988, Reckhow and Warren-Hicks 1996).
data using one or more of several
11-2 Index Development

Figure 11-1
1. Waterbody Classification —The Partitioning of Entire Water Resource The process for
physical and habitat data along with progressing from
biological data are used to group the classification
reference sites into homogeneous Class 1 Class 2 Class N of an estuary to
classes assessing the
health of the
estuary. Adapted
2. Metric Identification —Those from Paulsen et al.
Identification of Biological Attributes
metrics or attributes that are 1991.
ecologically relevant to assemblage
and zoogeography are identified
Metric 1 Value Metric 2 Value Metric NValue
3. Metric Calibration — Core metrics

are sensitive to pollution and are
informative of the ecological Evaluation and Calibration
relationships of the assemblage to
specific stressors or cumulative
impacts Core Metric Core Metric Core Metric
4. Index Development — Core

metrics, whose values vary in scale,
are transformed to dimensionless Aggregation
numbers for aggregation
Index
Score
Index Score
5. Threshold Establishment —The

Biocriteria
threshold (biocriterion) for Relative to
discriminating between impaired and Waterbody
unimpaired is determined to provide Class
a basis for assessment
classification methods. These methods EMAP Virginian Province

include cluster analysis and several
ordination methods such as: principal Natural environmental factors affecting
components analysis, correspondence species composition were examined in
analysis, and multidimensional scaling. the EMAP Virginian Province Project
(Paul et al. 1999, Strobel et al. 1995,
11.2.1 Existing Classifications Weisberg et al. 1993). Salinity has been
known to control estuarine organisms
With the growth of efforts to improve since the early days of marine biology.
environmental monitoring and develop Over 75% of the candidate measures
biocriteria, several successful were related significantly to salinity
classifications of estuarine and near- distributions (Figure 11-2). Correlation
coastal biological assemblages have been analysis was used to examine
developed. Here, we summarize several associations of habitat factors with
of these and integrate their findings on candidate biological metrics. Of the
classification of North American correlations between candidate
estuarine assemblages. measures and habitat factors,
Figure 11-2
Mean number
of species and
salinity at
EMAP-
Estuaries
sampling
stations in the
Virginian
Province (from
Weisberg et al.
1993). The
regression line
shown is the
expected
number of
species based
on the
polynomial
regression,
and was used
to estimate
salinity-
adjusted
species
richness
measures.
species richness was most strongly Cluster analysis of benthic infauna

correlated with salinity. indicated seven distinct habitats defined
by substrate and salinity. Polyhaline
In addition to salinity, the physical sand and mud, (salinities ($18 ‰) had
characteristics of estuarine sediments the highest mean Shannon-Wiener
and depth also influence benthic diversities, at 4.0 and 3.55, respectively
infaunal distribution and the (Weisberg et al. 1997).
accumulation of contaminants in
sediments (Rhoads 1974, Plumb 1981). EMAP Carolinian Province
EMAP collected sediment grain size,
silt-clay content, latitude, and depth From July - September 1995, a study
data to help interpret benthic response. was conducted to assess the
Although silt-clay content and depth environmental condition of estuaries in
were statistically significant, only the EMAP Carolinian Province (Hyland
salinity was deemed to have a et al. 1998, see Chapter 13). The
biologically significant influence on program sampled water depth, salinity,
benthic macroinvertebrates (r2 >0.025; and substrate classifications (% silt-clay)
Weisberg et al. 1993). Estuary type was as habitat indicators.
stratified in the project design, but
community differences due to estuary Species richness showed highly
type were not reported. significant correlations with latitude,
bottom salinity, and silt-clay/TOC
Chesapeake Bay sediment content. The Shannon-Wiener
index, H'(a combination of species
Weisberg et al. (1997) developed an richness and evenness), also showed
estuarine benthic index of biotic highly significant correlations (p #
integrity for the Chesapeake Bay. 0.0030) with bottom salinity as well as

with silt-clay fractions. As with sediment showing the most abundance
diversity, infaunal abundance showed in sand, mixed sediment, or muddy
highly significant correlations (p # bottoms.
0.0016) with the silt-clay and TOC
sediment content (Hyland et al. 1998). EMAP Louisianian Province
North Carolina Prior studies in the Gulf of Mexico had

shown salinity and sediment type to be
The North Carolina study was designed among the most important factors that
to compare biological metrics derived determine benthic infaunal
from three sampling methods (Ponar, relationships in Gulf of Mexico estuaries
epibenthic trawl, and sweep net). (Flint and Kalke 1985, Gaston et al. 1988,
Salinity was the only habitat Rabalais 1990, Rakocinski et al. 1991).
characteristic that was significantly Of the 182 total sites sampled, Pearson
correlated with biological metrics. Total correlations were performed between all
taxa showed a positive correlation with candidate measures and salinity,
salinity (Eaton 1994a; see Chapter 13). longitude of sampling site (as a measure
of geographical gradient), percent silt-
Puget Sound clay, and total organic carbon content of
sediments. Many of the correlations
The objective of the Puget Sound study were statistically significant at p < 0.05,
was to characterize benthic however, only salinity accounted for
macroinvertebrate communities into 20% or more of the variation (Summers
habitats classified as degraded and et al. 1993).
habitats that are relatively unimpaired,
which can then be classified as reference Southern California Bight
sites for the Sound (Llansó 1999).
The Southern California Coastal Water
The diverse assemblages sampled were Research Project sampled megabenthic
mainly associated with sediment type invertebrate assemblages, benthic
and water depth, reinforcing results infaunal assemblages, and demersal fish
from previous studies (Lie 1974). The assemblages to determine their
classes of sediments defined for the relationship to depth, latitude, and
Puget Sound estuaries were: sands, sediment types in the Southern
clays, and mixed. These three classes California Bight. There was no salinity
did not have exact boundaries, but gradient because the entire study area
instead overlapped at both ends of their was nearshore marine. Overall, depth
spectrums (Llansó 1999). Stations with was found to be the defining factor in
finer substrates had fewer species than the organization of each assemblage
those with coarser substrates. On (Allen et al. 1999, Bergen et al. 1999).
average, sand substrates supported
more species and abundance than did Sediment type was found to be a
clay, with deep sites having the lowest secondary factor in the organization of
abundance levels. Overall, clay stations benthic infaunal assemblages. This
in the southern part of Puget Sound finding could be attributed to the large
supported fewer species than many study area. In fact, within a constrained
other shallow clay locations. The depth range, sediment type may be a
majority of species were not restricted to more important factor (Bergen et al.
only one substrate, instead they were 1999). These findings are consistent
widely distributed in different types of with those of Snelgrove and Butman
(1994) which suggested that the 11.2.2 Assessing a priori
hydrodynamic environment and the Classifications
amount of organic material in the
sediment are more likely to be primary Although there is no serious doubt over
driving forces, with depth and sediment the influence of salinity, sediment, and
grain size as secondary correlates. depth on estuarine biota, the effects
must be characterized or calibrated to
Conclusions establish reference conditions. Several
approaches have been used, as outlined
Three habitat indicators have been in the examples in this chapter. Often,
demonstrated repeatedly to influence one of the first steps is a cluster analysis
biological assemblages of estuaries and of the species composition of the sites to
near coastal environments. In studies determine if sites can be broken down
where there was a salinity gradient, into groups (e.g., Weisberg et al. 1997,
salinity was found to be the most Smith et al. 2000). Sites may be divided
important habitat indicator. Depth and into groups defined by the important
substrate are also important and usually variables (e.g., salinity and sediment;
correlated, especially if there is a large Weisberg et al. 1997, depth; Smith et al.
depth gradient at the sample site. The 1999), or the groups may be separated
physical type of estuary (e.g., fjord, by discriminant function analysis (DFA)
lagoon, tidal river) has not been if simple, single relationships are not
demonstrated to be vital in wide sufficient (e.g., Engle and Summers
geographic studies, such as those 1999).
conducted by EMAP in the Virginian,
Louisianian, and Carolinian provinces, Another approach is to examine
but may not have been adequately correlations between environmental
tested. Therefore, the importance of variables and biological metrics
measuring estuary type, subregion, or calculated from the species data, so that
subprovinces is still questionable. reference expectations can be calibrated
accordingly. For example, species
Lessons learned from both EMAP and richness in estuaries is strongly affected
other independent studies conclude that by salinity (refer to Figure 11-2).
the basic classification of an index Weisberg et al. (1993) used the
should be by biogeograpical province, relationships of Figure 11-2 to develop a
salinity, substrate (silt-clay content, nonlinear regression of maximum
sediment grain size), and depth. The expected species richness on salinity.
effects of salinity, substrate, and depth Species richness was then adjusted by
should be tested within the study area to the salinity-specific maximum in further
determine whether all are required as development of their model of
habitat indicators in an individual area. impairment.
Moreover, decisions need to be made as
to the use of discrete classes or 11.3 Index Development
continuous covariates in statistical
analysis. If other classifications are An index for assessing sites can be
suspected to be important indicators of developed after classification of sites of
the health of a system, they should also the region is completed. Index
be tested (e.g., estuary type). development using the three
approaches followed in this chapter is
discussed here.

11.3.1 Multimetric Index perturbation; and (4) trophic or habit
measures for information on feeding
Step 1. Identify Potential Measures For strategies and guilds. Table 11-1 further
Each Assemblage. illustrates metrics for various
assemblages that have been useful in
Metrics allow the investigator to use estuaries. Components of Step 1
meaningful indicator attributes in include:
assessing the status of assemblages and
communities in response to < Review of the value ranges of
perturbation. The definition of a metric potential metrics, and elimination of
is a characteristic of the biota that those that have too many zero
changes in some predictable way with values in the population of reference
increased human influence (Barbour et sites to calculate the metric at a large
al. 1995). For a metric to be useful, it enough proportion of sites;
must have the following technical
attributes: (1) ecological relevance to the < Descriptive statistics (central
biological assemblage or community tendency, range, distribution,
under study and to the specified outliers) to characterize metric
program objectives, (2) sensitivity to performance within the population
stressors and provide a response that of reference sites of each site class;
can be discriminated from natural
variation. The purpose of using < Elimination of metrics that have too
multiple metrics to assess biological high variability in the reference site
condition is to aggregate and convey the population such that they cannot
information available regarding the discriminate among sites of different
elements and processes of aquatic condition.
communities.
Step 2. Select Robust Measures.
All metrics that have ecological
relevance to the assemblage under study Core metrics are those that will
and that respond to the targeted discriminate between good and poor
stressors are potential metrics for quality ecological conditions.
testing. From this “universe” of metrics, Discriminatory ability of biological
some will be eliminated because of metrics is evaluated by comparing the
insufficient data or because the range of distribution of each metric at a set of
values is not sufficient for reference sites with the distribution of
discrimination between natural metrics from a set of “known” stressed
variability and anthropogenic effects. sites (defined by physical and chemical
This step is taken to identify the characteristics) within each site class. If
candidate metrics that are most there is minimal or no overlap between
informative, and therefore, warrant the distributions, then the metric can be
further analysis. considered to be a strong discriminator
between reference and impaired
Representative metrics should be conditions (Figure 11-3).
selected from each of four primary
categories: (1) richness measures for Criteria are established to identify a
diversity or variety of the assemblage; population of “known” stressed sites
(2) composition measures for identity based on physical and chemical
and dominance; (3) tolerance measures measures of degradation. Criteria for
that represent sensitivity to
Tab le 11-1. Potential metrics for macrophytes, benthic macroinvertebrates, and fish that
could be considered for estuaries. Redundancy can be evaluated during the
calibration phase to eliminate overlapping metrics.
Richness Composition Tolerance Trophic/Habitat
< Not applicable < Not applicable < TSS < % cover
Macrophytes
< light < density of new

attenuation shoots
< Chlorophyll a < biomass
< DIN < stem counts
< DIP
< dominant taxa < # amphipods per < % < % or biomass

Macroinvertebrates
< taxa richness event polychaetes epibenthic

< Shannon-Wiener < amphipod biomass < polychaete < % or biomass
Diversity Index < mean abundance of biomass deposit feeders
< mean # of bivalves/site < % or biomass
Benthic
species < # of gastropods per suspension

< Pielou’s event feeders
Evenness Index
< dominant taxa < total # of species < #, % or < Proportion of

< taxa richness < # species in bottom biomass of planktivores
< # of estuarine trawl menhaden < Proportion of
spawners < # species comprising benthic feeders
Fish
< # anadronomous 90% of individuals < Proportion of

spawners piscivores
< total fish
exclusive of
Atlantic
menhaden
stressed sites can include (Weisberg et be easily compared by estimating their

al. 1993): discrimination efficiency (DE) or the
percentage of stressed sites below a
< Any sediment contaminant threshold representing the reference
exceeding the Long et al. (1995) sites. For example, DE could be
effects range-median (ER-M) measured as the percentage of stressed
concentration; sites below the 25th percentile of
reference sites, for a given metric.
< Survival in toxicity tests less than
80% of controls; Several studies have used tests of
statistical significance between
< Low dissolved oxygen; reference and stressed sites to select
metrics (e.g., Weisberg et al. 1997,
< Total sediment organic carbon > 3%. Hyland et al. 1998). Significance tests
should only be used if the sample size
Following identification of reference and (number of reference and stressed sites)
stressed sites, the biological metrics that is large enough that the test has
best discriminate between them are sufficient power to detect a meaningful
determined. difference.
Those metrics having the strongest

discriminatory power provide the most
confidence in assessing biological
condition of unknown sites. Metrics can

Figure 11-3
Hypothetical box
plot illustrating how
a successful metric
30 discriminates
between reference
26 and stressed sites.
22
Metric Value
18
14
10
6 Min-Max
25%-75%
2
Reference Stressed Median value
Step 3. Determine the best aggregation of percentile value, or other (e.g., trisected
core measures for indicating status and or quadrisected), to provide a range of
change in condition. scores. Those values that are closest to
the 95th percentile receive higher scores,
The purpose of an index is to provide a and those having a greater deviation
means of integrating information from from this percentile receive lower
the various measures of biological scores. For those metrics whose values
attributes (or metrics). Metrics vary in increase in response to perturbation the
their scale—they are integers, 5th percentile is used to remove outliers
percentages, or dimensionless numbers. and to form a basis for scoring.
Prior to developing an integrated index
for assessing biological condition, it is Alternative methods for scoring metrics
necessary to standardize core metrics via are currently in use in various parts of
transformation to unitless scores. The the U.S. for multimetric indexes. A
standardization assumes that each “trisection” of the scoring range has
metric has the same value and been well documented (Karr et al. 1986,
importance; i.e., they are weighted the Ohio EPA 1987, Weisberg et al. 1997,
same, and that a 50% change in one Hyland et al. 1998). More recent studies
metric is of equal value to assessment as are finding that a standardization of all
a 50% change in another. metrics as percentages of the 95th
percentile value yields the most
Where possible, the scoring criterion for sensitive index, because more
each metric is based on the distribution information of the component metrics is
of values in the population sites, which retained (e.g., Hughes et al. 1998).
include reference sites; for example, the
95th percentile of the data distribution is Aggregation of metric scores simplifies
commonly used to eliminate extreme management and decision making so
outliers. From this upper percentile, the that a single index value is used to
range of the metric values can be determine whether action is needed.
standardized as a percentage of the 95th Biological condition of waterbodies is
judged based on the summed index conditions and expectations for the
value (Karr et al. 1986). If the index classes, any decision on subdivision
value is above a criterion, then the should reflect the distribution of the
stream is judged as “optimal” or scores for the reference sites.
“excellent” in condition. The exact
nature of the action needed (e.g., Rating categories are used to assess the
restoration, mitigation, pollution condition of both reference and non-
enforcement) is not determined by the reference sites. Most of the reference
index value, but by analyses of the sites should be rated as good or very good
component metrics in addition to the in biological condition, which would be
raw data, and integrated with other as expected. However, a few reference
ecological information. Therefore, the sites may be given the rating as poor
index is not the sole determinant of sporadically among the collection dates.
impairment and diagnostics, but when If a “reference” site consistently receives
used in concert with the component a fair or poor rating, then the site should
information, strengthens the assessment be re-evaluated as to its proper
(Barbour et al. 1996b). Components of assignment. Putative reference sites
Step 3 include: may be rated “poor” for several reasons:
< Development of scoring criteria for < Natural variability — owing to

each metric (within each site class) seasonal, spatial, and random
from the appropriate percentile of biological events, any reference site
the data distribution (Figure 11-4). If may score below the reference
the metric is associated with a population 10th percentile. If due to
significant covariate such as estuary natural variability, a low score
size, depth, or salinity a scatterplot should occur 10% of the time or less;
of the metric and covariate and a
moving estimate of the appropriate < Impairment — stressors that were
percentile, are used to determine not detected in previous sampling or
scoring criteria as a function of the surveys may occur at a “reference”
covariate (e.g., Weisberg et al. 1993); site; for example, episodic non-point
source pollution or historical
< Testing the ability of the final index contamination may be present at a
to discriminate between populations site;
of reference and anthropogenically
affected (stressed) sites. < Non-representative site — reference
sites are intended to be
Step 4. Index thresholds for assessment and representative of their class. If there
biocriteria. are no anthropogenic stressors, yet a
“reference” site consistently scores
The multimetric index value for a site is outside the range of the rest of the
a summation of the scores of the metrics reference population, the site may
and has a finite range within each site be a special or unique case, or it may
class and index period, depending on have been misclassified and actually
the maximum possible score of the belong to another class of sites.
metrics (Barbour et al. 1996a). This
range can be subdivided into any
number of categories corresponding to
various levels of impairment. Because
the metrics are normalized to reference

Figure 11-4
maximum
Basis of metric
95th percentile 100 scores using the
5
4 95th percentile as a
standard.
3
3
2
(
observed value
95th value
X 100
)
1
1
0
All Trisection Quadrisection Percentage
Sites of standard
Scoring Methods
Components of Step 4 include: Once the framework for bioassessment

is in place, conducting bioassessments
Assessment categories are becomes relatively routine. Either a
subdivided from the range of targeted design that focuses on site-
possible scores for each site class. specific problems or a probability-based
Categories should be proportional to design, which is appropriate for 305(b),
the interquartile range (or standard area-wide, and watershed monitoring,
deviation) of total scores in the can be done efficiently. Routine
reference sites. Thus, reference sites monitoring of reference sites should be
with a small interquartile range based on a random selection procedure,
which will allow for cost efficiencies in
(small s.d.; small coefficient of
sampling while monitoring the status of
variation) would yield more
the reference condition. Potential
assessment categories than a more
reference sites of each class would be
variable reference population; randomly selected for sampling, so that
an unbiased estimate of reference
The validity of biological condition condition can be developed. A
categories is evaluated by comparing randomized subset of reference sites can
the index scores of the reference and be resampled at some regular interval
known stressed sites to those (e.g., a 4-year cycle) to provide
categories. If reference sites are not information on trends in reference sites.
rated good or very good, then some
adjustment in either the biological Example 1: Chesapeake Bay Index
condition designations or the listing Development
of reference sites may be necessary;
For the Chesapeake Bay, a separate
Confidence intervals are estimated benthic index was developed for each of
for the multimetric index to help seven habitats: tidal fresh, oligohaline,
determine biological condition for low mesohaline, high mesohaline sand,
sites that fall in close proximity to a high mesohaline mud, polyhaline sand,
threshold. Precision and sensitivity and polyhaline mud (Weisberg et al.
are determined from replicate 1997). These habitats had been
samples, and are important for identified as separate assemblages in
estimating the confidence of the classification step.
individual assessments.
Reference and stressed sites were Example 2: Louisiana and Maryland
identified by the following: from Fish Indexes
existing Chesapeake Bay data, no
reference sites could be in highly Several states are developing fish
developed (urban) watersheds or near indexes of biotic integrity (IBI) for
known point-source discharges, no estuarine species. The multimetric
reference site could have organic carbon Index of Biotic Integrity (IBI) concept
content > 2%, no reference site could was originally developed for fresh
have any sediment contaminants water streams (Karr 1981), and has been
exceeding the Long et al. (1995) effects modified and applied to a Louisiana
range-median (ER-M) concentration, no estuary (Thompson and Fitzhugh 1986).
reference site could have low dissolved The strength of this index is that many
oxygen, and no reference site could factors affecting biological integrity can
exhibit any sediment toxicity. Stressed be measured in fish (e.g., community
sites were defined as those with any composition, relative abundance, health,
contaminant exceeding the ER-M etc.). This proposed estuarine IBI
concentration and measured sediment maintains the same three main
toxicity, or total organic carbon categories as those of the fresh water
exceeded 3%, or dissolved oxygen was IBI: species composition, trophic
low, < 2-mgL-1 (Weisberg et al. 1997). composition, and fish condition.
However, the metrics are modified to
Index development proceeded through reflect estuarine habitats and fish
the steps: assemblages. In addition, because
estuarine systems exhibit a high degree
Step 1. 17 candidate metrics were of seasonality in their fish fauna, a
identified based on the paradigms of measure of seasonal variability was
Pearson and Rosenberg (1978). incorporated. The metrics for estuaries
are based on life history and habitat
Step 2. 15 of the 17 metrics could requirements similar to those of the
distinguish between reference sites and fresh water IBI. Proposed metrics from
stressed sites in one or more of the seven Thompson and Fitzhugh (1986) for
habitats. estuarine communities are listed in
Table 11-2. A similar fish Index of Biotic
Step 3. Four to seven of the metrics were Integrity is being adapted for
used for an index specific to each habitat application in estuarine and coastal
type. Scoring of metrics was on a 5-3-1 marine habitats on the Gulf Coast of
scale, with metric values greater than Texas (Guillen 1995).
the reference site median scored as 5;
between the 5th and the median of the The state of Maryland has also
reference sites scored as 3; and below developed a fish Index of Biotic
the 5th percentile scored as 1. Integrity that is more rapid and less
expensive to apply (Jordan et al. 1992).
Step 4. The index was able to correctly This fish IBI is comprised of nine
classify as reference or stressed 93% of metrics (Table 11-3) that can be
an independent validation data set that compared to measurements of the
had not been used to develop the index. physical environment such as dissolved
oxygen and land use.

Table 11-2. Estuarine fish IBI metrics proposed by Thompson and Fitzhugh (1986).
Community Metric
Structure/Function
Species composition Total number of fish species

Number and identity of resident estuarine species
Number and identity of marine species
Number and identity of sciaenids
Number and identity of freshwater species
Proportion of individuals as bay anchovy
Measure of seasonal overlap of fish community
Number of species needed to make up 90% of collection
Trophic composition Proportion of individuals as generalized benthic feeders

(for adults of species) Proportion of individuals as generalized plankton grazers
Proportion of individuals as top carnivores
Fish abundance and Proportion of young of year in sample or number of individuals

condition in sample
Proportion of individuals with disease, tumors, fin damage, and
other anomalies
The results of some preliminary analyses with intermediate sites not used for
from areas in the Chesapeake Bay with discriminant model building (Engle et
salinities ranging from 0-to-16 ppt al. 1994, Weisberg et al. 1993).
indicate that the Maryland IBI can be
used to identify large scale spatial and The classification step for the EMAP
temporal trends in biological integrity discriminant models consisted of
and that the index responds to water examining associations between benthic
quality (DO) and land use impacts. macroinvertebrate metrics and physical
habitat measures of salinity, sediment
11.3.2 Discriminant Model Index grain size, and depth. Only salinity had
a strong relationship with the taxa
Discriminant Model Approach richness metric; taxa richness was
estimated as the percent of taxa
The discriminant model approach was expected, adjusted for salinity (refer to
used by EMAP to develop benthic Figure 11-2).
condition indexes for the Virginian
Province (Mid-Atlantic) and for the Discriminant Model Analysis
Louisianian Province (Gulf Coast)
(Engle et al. 1994, Summers et al. 1993, The discriminant model analysis is a
Weisberg et al. 1993, Paul et al. 1999) multivariate procedure that attempts to
based on defined reference sites. Sets of build a model that will predict the
minimally impaired sites; i.e., membership of a site into two or more
"reference" and impaired sites were predetermined classes. In the example
identified; impaired sites were affected used in EMAP, the classes were
by either hypoxia (DO <2 mgL-1 ); toxic reference and impaired sites (by low
sediments; or sediment contamination DO, toxicity or metal contamination).
above the ER-M threshold. Minimally The model procedure attempts to find a
impaired sites were defined to have DO linear combination of input variables
>5 mgL-1 and no detectable toxicity or (biological metrics) that best predicts
contamination. The two site types membership in the class. Alternative
represented the ends of a continuum,
Table 11-3. Maryland estuarine fish IBI metrics.
Community Metric Response

Structure/Function to
Impairment
Species composition Total number of species reduced

Number of species in bottom trawl reduced
Number of species comprising 90 percent of reduced
individuals
Trophic composition Proportion of planktivores increased

(for adults of species) Proportion of benthic feeders decreased
Proportion of piscivores decreased
Fish abundance and Number of estuarine spawners decreased

condition Number of anadromous spawners decreased
Total fish exclusive of Atlantic menhaden decreased
models are tested by estimating the 1994, 1995, Paul et al. 1999). Inclusion of
proportion of sites (from the several years of monitoring data in both
model-building data set) that are provinces produced more robust and
misclassified. The best model usually reliable models. In the Virginian
has the lowest misclassification rate. A Province, the robust calibration data set
test of a model requires an independent consisted of 60 sites (30 each).
test data set that was not used to build
the model. An improved index was created to be
applicable across a variety of estuarine
EMAP built discriminant models using environments in the Gulf of Mexico
benthic metrics in a stepwise model (Engle and Summers 1999). The
building approach. The models used statistical approach described in Engle
three to five metrics in the Louisianian and Summers (1999) proved to be
and Virginian provinces respectively, applicable throughout the estuaries in
and both models used taxa richness the northern Gulf of Mexico. This
(Engle et al. 1994, Weisberg et al. 1993). benthic index was also validated
The benthic indexes were then independently by Rakoncinski (1997),
calculated as the discriminant score of a who compared results of canonical
site and standardized on a scale of 1 to correspondence analysis (CCA) with
10. data from EMAP-E (1991-1992), using
the index developed in Engle et al. 1994
Performance of the discriminant models (Engle and Summers 1999).
was good in distinguishing reference
from impaired sites in the calibration 11.3.3 Index Derived from
data: 100% for the Gulf of Mexico sites Multivariate Ordination
(Engle et al. 1994; n = 16 sites) and 86-
93% for the Virginian Province sites An index for biocriteria was derived by
(Weisberg et al. 1993; n = 33 sites). Smith et al. (2000) using multivariate
When tested with validation data ordination to derive a pollution
collected in subsequent years, however, gradient, which in turn was used to
both sets or models failed to predict develop an index. The approach was
adequately and had to be redeveloped developed with benthic
(Engle and Summers 1999, Strobel et al. macroinvertebrates from the Southern

California Bight (Smith et al. 2000; see for the introduction of the
also 11.2.1, p. 11-5), and is currently transformation exponent f) to the
being applied to demersal fish from the Hilsenhoff Biotic Index. Biocriteria can
same waters (Allen and Smith 2000). be assigned to index values; for
The approach is computationally example, if the index is defined in the
intensive and rather complex. We will range from 0 (unpolluted) to 100
describe the result first (the index and its (severely polluted), then a criterion for
components), and then briefly describe Class A estuarine waters might be
how the components themselves are values 25.
derived.
The steps below outline the derivation
The central assumption of this approach of the tolerance values pi. A data set is
is that each species has a tolerance for required with sites that span a range
pollution, and that if the pollution from unpolluted to severely polluted.
tolerance is known for sufficiently large In the Southern California Bight, these
set of species, it is possible to infer the were defined by sediment contaminant
degree of degradation from species levels above and below the effects range
composition and the tolerances. This is median (ER-M) and effects range low
the basis of the familiar Hilsenhoff Biotic
(ER-L) concentrations (Long et al. 1995).
Index (HBI; Hilsenhoff 1987) of
Levels of a contaminant below the ER-L,
freshwater bioassessment, as well as of
several metrics in the multimetric between the ER-L and ER-M, and above
approach. For example, capitellid the ER-M are rarely, occasionally, and
polychaetes are known to be tolerant to frequently, respectively, associated with
organic pollution (BOD). The index adverse effects. Impacted sites had six
used by Smith et al. is a weighted of eight selected contaminants (Cu, Pb,
average tolerance value of all species Ni, Zn, Cd, Cr, PCB, and DDT) above
found in a sample, weighted by the ER-M. Reference sites consisted of
abundance of the species: stations lying outside of POTW
discharge areas and with no more than
one selected contaminant above the ER-
Equation 11-1. L for a contaminant.
n
¦ a sif p i The data must be divided into two sets:

Is i 1 a calibration subset and a test subset.
n
¦
i 1
a sif Step 1. Ordination analysis of species
abundance (calibration data).
where Is is the index value for sample s,
n is the number of species in sample s, asi Ordination analysis produces a plot of
is the abundance of species i in sample s, sites in ordination space (Figure 11-5).
pi is the tolerance value of species i, and Distances between pairs of points are
the exponent f is used to downweight proportional to the dissimilarity of
extreme abundances. If f is zero, then species composition in the
corresponding samples: samples with
the index is not weighted by abundance
very similar composition will be close
(Smith et al. 2000, Allen and Smith
together in the ordination diagram. If
2000).
the species are associated with the
pollution gradient, the sites will define a
The index of equation (11-1) is
gradient, with polluted sites at one end
computationally almost identical (except
Figure 11-5
Steps 1-3.
Step 1: ordination Establishing site
scores on a
contamination
gradient. The
p p gradient is
p 0 established between
• 10 “contaminated” end
Ordination Axis 2
reference (“r”) and

• contaminated (“p”)
sites as plotted in
• p p Step 2: gradient ordination space.
Dots are sites not
designated as either
50 • p
reference or
contaminated. The
projection of site “x”
r r on the gradient
r •x (dotted line) yields
r its site score.
r Step 3: project site scores Adapted from Smith
0 et al. 2000.
r r
“reference” end
Ordination Axis 1
and unpolluted sites at the other (Figure Step 5. Compute tolerance values for each
11-5). species.
Each species has an “average” position

Step 2. Find the pollution gradient. on the pollution gradient. These species
positions are the tolerance values (pi) of
The two ends of the pollution gradient Equation 11-1. Site scores calculated in
are defined as the average positions in Step 4 give each site a position on the
ordination space of the unpolluted and pollution gradient. The abundance of a
polluted sites, respectively. These ends species at each observation can be
are connected by a line, which plotted against the site scores (Figure
represents the pollution gradient as 11-6). The species position on the
expressed by the observed species gradient, or the tolerance value pi, is the
compositions. abundance-weighted average position
for the species over all sites.
Step 3. Project all calibration observations
onto the pollution-effects gradient. Step 6. Compute the f parameter.
The position of each site in the The f-parameter is iterated

ordination space is projected onto the simultaneously with the pi in an
gradient. This projection is the site score optimization procedure (Smith et al.
of the calibration sites (Figure 11-5). 2000).
Step 4. Rescale the projections. The species tolerance scores were in

turn used to predict the Benthic
Site scores are scaled from 0 (“least Response Index (BRI) according to
polluted”) to 100 (“most polluted”). Equation 11-1. The BRI is the position
of a site on the contamination gradient,
or the predicted value of the site score

Figure 11-6
Step 5.
100 Computing the
tolerance values.
Abundance of
Species A and
site scores (from
Figure 11-5) of all
sites where
Abundance of Species A
Species A
occurs. The
abundance-
• weighted average
score over all
• ••• sites is Species
• • A’s pollution
•• • •• • tolerance score
•• •••
• •• • • (arrow). This
• • • ••• •• ••••••
• •••
••
example shows a
highly tolerant
0
•••••• •• ••• •• •••••• •• •• •• •• • •• •• • •• • •• • •
•• •••••• ••• species, which
occurs in greatest
abundances at
0 100 the most polluted
sites. Adapted
Site Scores from Smith et al.
2000.
calculated in Step 4. Actual site scores

(Step 4) are calculated only for the Smith et al. estimated tolerance values
calibration data; site score is predicted as for over 450 marine species from
BRI for all assessment sites. southern California. The BRI
contamination score can be calculated
The BRI was developed separately for 3 for any new site from species
depth zones: 10-35-m, 25-130-m, and abundance data at the site. The BRI has
110-324-m. Earlier work had shown that a range from 0 (unpolluted) to 100
benthic communities off Southern (severely polluted) and biocriteria can
California could be classified by depth be set at selected values for specific
and sediment type (see Section 11.2.1, p. aquatic life uses of coastal waters of
11-5). Sediment type was secondary, Southern California. Reference sites
and was not deemed to have a strong had BRI values < 25, and all severely
enough effect to justify further contaminated sites had BRI > 36 (Smith
categorization of the data set. et al. 2000). The reference values could
form the basis of biocriteria for the
The tolerance index developed by Smith region.
et al. was then tested with the
independent data (not used to develop
the index). The independent test
showed that the model was largely
correct in predicting position along the
contamination gradient. For further
details of calculations and formulas, see
Smith et al. (2000). The approach is
currently being extended to demersal
fish from the same region (Allen and
Smith 2000).
Chapter 12
Quality Assurance:
Design, Precision and
Management
Quality assurance (QA) is an integrated QA is accomplished through:

program for ensuring the reliability of
monitoring and measurement data and < Program design;
includes quality control. Quality control
(QC) refers to operational procedures for < Investigator training;
obtaining prescribed standards of
performance in the monitoring and < Standardized data gathering and
measurement process. Specific QC processing procedures;
elements can be developed for most, if
not all, project activities. All project < Verification of data reproducibility;
activities, from sampling (data
collection) and laboratory analysis to < Instrument calibration and
statistical analysis and reporting, are maintenance.
potential error sources (Peters 1988).
Because error is cumulative and can As outlined below, QA requirements
significantly affect the results of a apply to all activities in an ecological
project, all possible efforts must be made study. More detailed guidance and
to control it. Therefore, quality examples for QA activities should be
assurance is a continuous process that obtained from USEPA (1994c, and
should be implemented throughout the 1998a); more general guidance is
entire development and operation of a outlined by USEPA (1993b).
program.
12.1 Program Design
The purpose of an overall quality
assurance project plan (QAPP), A central component of QA is overall
containing specific QC elements and study design which includes
activities, is to minimize—and when formulation of questions and
possible eliminate—the potential for hypotheses, experimental design, and
error. Additionally, there are objective development of analysis approaches.
mechanisms for evaluating activities The classical approach by which
relative to pre-established measurement scientists plan research consists of the
quality objectives and other project following steps:
goals. The appropriateness of the
investigator's methods and procedures < Statement of the problem to be
and the quality of the data to be resolved;
obtained must be ensured before the
results can be accepted and used in < Formulation of alternative
decision making. hypotheses that will explain the
phenomena or, in the case of
problems that do not involve so that measurement error can always
elaboration of processes, formulation be estimated from a subset of sites.
of specific research questions; Repeated measurement at 10% or more
of sites is common among many
< Establishment of boundaries within monitoring programs.
which to resolve the problem;
12.1.2 Establishment of Uncertainty
< Formulation of an experimental or Limits
study design that will falsify one or
more hypotheses or answer the The level of uncertainty associated with
specific research questions; environmental measurements (due to
natural variability, sampling error,
< Establishment of uncertainty limits measurement error, or other sources of
including setting acceptable uncertainty) propagates directly to the
probabilities of type I and type II uncertainty of inferences and
errors for statistical hypothesis conclusions that can be made from the
testing; data. Establishing the limits of
statistical uncertainty for conclusions
< Optimization of the study design also sets limits for the data to be
including power analysis of the collected (also known as Data Quality
statistical design. Objectives [DQOs]; Chaloud and Peck
1994). As mentioned in Chapter 5, there
Experimental advances in basic sciences is a close association between sampling
have not included the last two steps intensity and uncertainty. Reducing
because uncertainty limits were uncertainty usually results in greater
inappropriate or unknown. costs. Assessing uncertainty, and
Examination of experimental advances optimizing the study design (below)
also reveals that a high degree of require at least pilot data in hand, if not
creativity and insight is required to results from one year or more of
formulate hypotheses and study monitoring.
designs; no formal planning process or
"cookbook" can guarantee creativity and As an example of uncertainty limits,
insight. Nevertheless, documentation of USEPA’s EMAP program established
the planning process and a complete the following (Chaloud and Peck 1994):
explanation of the conceptual
framework help others evaluate the < Estimate the status of a population
validity of scientific and technical of resources with 95% confidence
achievements. intervals that are within 10% of the
estimate;
12.1.1 Formulation of a Study Design
< Determine average change in status
A study design is developed to answer of 20% over 10 years with 95%
the specific monitoring questions confidence and statistical power of
developed in formulating the questions 0.8.
and objectives. Sampling design
considerations were discussed in EMAP selected 95% confidence
Chapter 5. intervals, however, there is nothing
“scientific” about choosing 95%
For quality assurance, some effort will intervals over, say, 90% or 99%. The
always be required for repeated samples second limit above, determining
12-2 Quality Assurance: Design, Precision and Management

change, implies that EMAP managers really false. The magnitude of a Type I
were only willing to conclude a false error is represented by " and the
change in status 1 time out of 20 (Type I magnitude of a Type II error is
error; false positive), but were willing to represented by $. Decision errors are
conclude a false lack of change 1 time the result of measurement and sampling
out of 5 (Type II error, false negative). design errors that were described in
Section 12.1.1. A proper balance
12.1.3 Optimizing the Study Design: between sampling and measurement
Evaluation of Statistical Power errors should be maintained because
accuracy limits effective sample size
A principal aspect of probability and vice versa (Blalock 1979).
sampling is determining how many
samples will be required to achieve the Comparison of Significance Level
monitoring goals and what is the and Power
probability of making an incorrect
decision based on the monitoring Regardless of the statistical test chosen
results. The primary tool for conducting for analyzing the data, the analyst must
these analyses is statistical power select the significance level of the test.
analysis. Evaluating statistical power is That is, the analyst must determine
key to developing data quality criteria what error level is acceptable. The
and performance specifications for probability of making a Type I error is
decision making (USEPA 1996b) as well equal to the significance level (") of the
as evaluating the performance of test and is selected by the data analyst.
existing monitoring programs (USEPA In many cases, managers or analysts
1992). Power analysis provides an define 1-" to be in the range of 0.90 to
evaluation of the ability to detect 0.99 (e.g., a confidence level of 90 to
statistically significant differences in a 99%), although there have been
measured monitoring variable. The environmental applications where 1-"
importance of this analysis can be seen has been set to 0.80. Selecting a 95%
by examining the possible outcomes of a confidence level implies that the analyst
statistical test. The null hypothesis (Ho) will reject the Ho when Ho is really true,
is the root of hypothesis testing. i.e., a false positive, 5% of the time.
Traditionally, null hypotheses are
statements of no change, no effect, or no Type II error depends on the
difference. For example, the mean significance level, sample size, number
abundance at a test site is equal to the of replicates, variability, and which
mean abundance of the reference sites. alternative hypothesis is true. The
The alternative hypothesis (Ha ) is power of a test (1-$) is defined as the
counter to Ho, traditionally being probability of correctly rejecting Ho
statements of change, effect, or when Ho is false. In general, for a fixed
difference. Upon rejecting Ho, Ha would sample size, " and $ vary inversely.
be accepted. Power can be increased ($ can be
reduced) by increasing the sample size
The two types of decision errors that or number of replicates. Figure 12-1
could be made in hypothesis testing are illustrates this relationship. Suppose
depicted in Table 12-1. A Type I error the interest is in testing whether there is
(i.e., false positive) occurs when Ho is a significant difference between the
rejected although Ho is really true. A means from two independent random
Type II error (i.e., false negative) occurs samples. As the difference in the two
when Ho is not rejected although Ho is sample means increases (as indicated on
Table 12-1. Errors in hypothesis testing.
State of the population (truth)

Decision
Ho is True Ho is False
Accept Ho 1-
(Confidence level) (Type II error)
Reject Ho 1-
(Significance level) (Power)
(Type I error)
Figure 12-1
Effect of n2 critical value for n2
increasing sample
critical value for n1
size from n1 to n2
on power. The n1
curves represent
the probability a. Reference
distribution of the sample
{
sample means rejection region, α1 , for n1
from 2 samples,
{
reference and test, probability of Type
II error for n2
and for 2 sample rejection region, α2 , for n2
n2
sizes n1 and n2
where n2 > n1.
n1
b. Test sample
probability of Type II
error (false negative)
for n1
the x-axis), the probability of rejecting Basic Assumptions

Ho, the power, increases. If the real
difference between the two sample Usually, several assumptions regarding
means is zero, the probability of data distribution and variability must
rejecting Ho is equal to the significance be made to determine the sample size.
level, . Figure 12-1a shows the general Applying any of the equations
relationship between and if is described in this chapter is difficult
changed. Figure 12-1b shows the when no historical data set exists to
relationship between and if the quantify initial estimates of proportions,
sample size is increased. The tradition standard deviations, means, or
of 95% confidence ( = 0.05) is entirely coefficients of variation. To estimate
arbitrary; there is no scientific these parameters, Cochran (1963)
requirement that confidence be set at recommends four sources:
95%. Indeed, for environmental
protection, power is at least as Existing information on the same
important—and possibly more
population or a similar population;
important—than confidence (Peterman
1990, Fairweather 1991).
A two-step sample. Use the first-
step sampling results to estimate the
needed factors, for best design, of

the second step. Use data from both be compared with a number of
steps to estimate the final precision statistical tests including the parametric
of the characteristic(s) sampled; two-sample t-test, the nonparametric
Mann-Whitney test, and two-sample
A "pilot study" on a "convenient" or test for proportions (USEPA 1996b). In
"meaningful" subsample. Use the this case, two independent random
results to estimate the needed samples are taken and a hypothesis test
factors. Here the results of the pilot is used to determine whether there has
study generally cannot be used in been a significant change. To compute
the calculation of the final precision sample sizes for comparing two
because often the pilot sample is not proportions, p1 and p2, it is necessary to
representative of the entire provide a best estimate for p1 and p2, as
population to be sampled; well as specifying the significance level
and power (1-). Recall that power is
Informed judgment, or an educated equal to the probability of rejecting Ho
guess. when Ho is false. Given this
information, the analyst substitutes
For evaluating existing programs, these values into the following equation
proportions, standard deviations, (Snedecor and Cochran 1980):
means, etc. would be estimated from
actual data. Equation 12-1.
Some assumptions might result in

sample size estimates that are too high
or too low. Depending on the sampling
where Z and Z2 correspond to the
cost and cost for not sampling enough
normal deviate. Common values of (Z
data, it must be decided whether to
+ Z2)2 are summarized in Table 12-2.
make conservative or "best-value"
To account for p1 and p2 being
assumptions. Because of the fixed
estimated, t could be substituted for Z.
mobilization costs, it is probably cheaper
to collect a few extra samples the first In lieu of an iterative calculation,
time than to realize later that additional Snedecor and Cochran (1980) propose
data are needed. In most cases, the the following approach: (1) compute no
analyst should probably consider using Equation 12-1; (2) round no up to
evaluating a range of assumptions the next highest integer, f; and (3)
regarding the impact of sample size and multiply no by (f+3)/(f+1) to derive the
overall program cost. USEPA final estimate of n.
recommends that if the analyst lacks a
background in statistics, he/she should To compare the mean from two random
consult with a trained statistician to be _samples
_ to detect a change of ; i.e.,
certain that the approach, design, and x2-x1, the following equation is used:
assumptions are appropriate to the task
at hand. Equation 12-2.
Simple Comparison of Proportions and

Means from Two Samples
The proportion (e.g., percent dominant

taxon) or mean (e.g., mean number of
Common values of (Z + Z2)2 are
EPT taxa) of two data sets data sets can
summarized in Table 12-2. To account
Table 12-2. Common values of (Z + Z2)2 for estimating sample size for use with Equations 12-1
and 12-2 (Snedecor and Cochran 1980).
Power, for One-sided Test for Two-sided Test
1- 0.01 0.05 0.10 0.01 0.05 0.10
0.80 10.04 6.18 4.51 11.68 7.85 6.18
0.85 11.31 7.19 5.37 13.05 8.98 7.19
0.90 13.02 8.56 6.57 14.88 10.51 8.56
0.95 15.77 10.82 8.56 17.81 12.99 10.82
0.99 21.65 15.77 13.02 24.03 18.37 15.77
for s1 and s2 being estimated, Z should estimated are not normally distributed.
be replaced with t. In lieu of an iterative The Student's t statistic (t/2,n-1) is used
calculation, Snedecor and Cochran to compute symmetric confidence
(1980) propose the following approach: intervals for the population mean, :
(1) compute no using Equation 12-2; (2)
round no up to the next highest integer, Equation 12-4.
f; and (3) multiply no by (f+3)/(f+1) to
derive the final estimate of n.
A special case of Equation 12-2 arises for

biocriteria, when we compare the mean
of a sample to determine if the value is This equation is appropriate if the
below some set limit, that is, if the site is samples are normally distributed or the
impaired or below a reference threshold. sample size is greater than 30
The threshold is fixed by previous (Wonnacott and Wonnacott 1969),
investigations and decisions, and is not although Helsel and Hirsch (1992)
a random variable. We ask now suggest that highly skewed data might
whether _ we can detect a change of ; require more than 100 observations.
i.e., C-x1, where C is the biocriteria limit:
Although several approaches exist to
Equation 12-3.
estimate confidence levels for any
percentile, many rely on assuming a
normal or lognormal distribution. The
approach presented here (Conover
In Equation 12-3, Z is most often one- 1980) for more than 20 observations
tailed, because the concern is only does not rely on these assumptions.
whether the value is below the Conover (1980) also provides a
threshold. procedure for smaller sample sizes. To
calculate the confidence interval
Sample Size Calculations for Means and corresponding to the median, lower
Proportions quartile, or upper quartile, the following
procedure is used.
For large sample sizes or samples that
are normally distributed, symmetric 1. Order the data from smallest to
confidence intervals for the mean are largest observation such that
appropriate. This is because the
distribution of the sample mean will
x 1 ≤ ... ≤ x r ≤ ... ≤ x p ≤ ... x s ≤ ... ≤ x n
approach a normal distribution even if
the data from which the mean is

where xp corresponds to the median; i.e., document personnel responsibilities
p=0.5, lower quartile; i.e., p=0.25, or and duties and clearly delineate project
upper quartile; i.e., p=0.75. organization and lines of communica-
tion (USEPA 1998a). A time line
2. Compute the values of r* and s* as illustrating completion dates for major
project milestones or other tasks can be
Equation 12-5. a tremendously useful tool to track
r * = n p + Z a / 2 ( n p (1 − p )) 0 . 5 project organization and progress.
s * = n p + Z a / 2 ( n p ( 1 − p )) 0 .5
12.2.2 Resources
where Z/2 is selected from a normal
distribution table. Laboratory facilities, adequate field
equipment, supplies, and services
3. Round r* and s* up to the next should be in place and operationally
highest integers r and s. The 1- consistent with the designed purposes
lower and upper confidence limits of the program so that high-quality
for xp are xr and xs, respectively. environmental data can be generated
and processed in an efficient and cost-
It can be seen from Equation 12-5 that effective manner (USEPA 1992).
estimation of medians or quartiles from Adequate taxonomic references and
small samples can result in large scientific literature should be available
confidence intervals for the estimate. to support laboratory work, data
For example, the 90% confidence processing, and interpretation.
interval for the lower quartile of a
sample of n=10 covers the first 5
observations. A sample of less than 10
12.3 Operational Quality
observations would have a confidence Control
interval extending below the smallest
observation. This is the reasoning Protocols should be developed for
behind a general “rule of thumb” that designing a data base and for screening,
estimation of reference conditions archiving, and documenting data. Data
should be based on a sample of 10 or screening identifies questionable data
more sites, if at all possible. Figure 12-2 based on expected values and obvious
gives example sample size calculations outliers. Screening is especially
for comparing proportions and important if data are gathered from a
population means. variety of sources and the original
investigators and data sheets are no
12.2 Management longer available. Figure 12-3 defines the
qualitative and quantitative data
12.2.1 Personnel characteristics that are most often used
to describe data quality.
Trained and experienced biologists
should be available to provide thorough These measurement quality indicators
evaluations, provide support for various require a priori consideration and
activities, and serve as QC checks. They definition before the data collection
should have training and experience begins. Taken collectively, they provide
a summary characterization of the data
commensurate with the needs of the quality needed for a particular
program. At least one staff member environmental decision. Duplication of
should be familiar with establishing a approximately 10% of the total
QA framework. QA programs should sampling effort is a common level for
Figure 12-2
Example 1—Sample size calculation for comparing proportions
Example
To detect a difference in prop ortions of 0 .20 w ith a two -sided test, " equal sample size
calculations for
to 0.05, 1-$ equal to 0.90, and an estim ate of p 1 and p 2 equal to 0.4 and 0.6,
comparing
n o is computed from Equation 12-1 as proportions
and population
means.
Ro und ing 12 6.1 to the next highest integ er, f is equal to 127, and n is
computed as 126.1 x 130/128 or 128.1. Therefore 129 samples in each
random sam ple, or 258 total sam ples, a re needed to dete ct a difference in
proportions of 0.2. Since these are proportions, the result means that the
total count in the sample must be at least 129. For example, to detect the
above difference in the pro portion of do m inant ta xon (e .g., benth ic
macroinvertebrates or fish) of two sites, at least 129 individuals must be
counted and identified in each estua ry.
The exam ple illustrates that a statis tica lly significant difference can be easily
detec ted in proportions if su ffic ient individuals are sam pled. H ow ever, it is
doubtful that a difference betw een 40% and 60% in dom inant ta xon is
biologically m eaningful.
Example 2—S ample size calculation for comparing population mean

abundance
To detect a difference of 20 in mean abundance with a two-sided test. The

stan dard deviation, s, was estimated as 30 for both samples based on
prev ious studies; " was selected as 0.05; and 1-$ was selec ted as 0.90.
Substituting these values into Equation 12-2 yields
Ro und ing 47 .3 to the nex t highe st integ er, f is equal to 48,

and n is computed as 47.3 x 51/49 or 49.2. Therefore 50
sam ples in each rando m sam ple, or 100 total samples, are
nee ded to detect a differe nce of 20 .
operational QC. Replication of samples 12.3.1 Field Operations

at a randomly selected subset of field
sites (usually, 10 percent of the total For the field operations aspect of an
number is considered appropriate) is ecological study, the major QC elements
used to estimate precision, and are: instrument calibration and
representativeness of the samples and maintenance, crew training and
the methods. Splitting samples into evaluation, field equipment, sample
subsamples can be used to check handling, and additional effort checks.
precision of the methodology, and The potential errors in field operations
reprocessing of finished samples is used range from personnel deficiencies to
to check accuracy of laboratory equipment problems. Field notes are
operations. integral to the documentation of

Figure 12-3
< Precision - The level of agreement am ong repeated
Six qualitative and
quantitative data measurem ents of the same characteristic.
characteristics
usually employed < Accuracy - The level of agreement between the true and the
to describe data measured value, where the divergence between the two is
quality. referred to as bias.
< Representativeness - The degree to which the collected data

accurately reflect the true system or population.
< Com pleteness - The amount of data collected compared to the

amount expected under ideal conditions.
< Com parab ility - The degree to which data from one source can be
compared to other, similar sources.
< Measu rability - The degree to which measured data exceed the
detection limits of the analytical methodologies employed; often a
function of the sensitivity of instrumentation.
activities and can be a potential error 12.3.3 Data Analysis

source if incorrect recording occurs.
Training is one of the most important Errors can occur if inappropriate
QC elements for field operations. statistics are used to analyze the data.
Establishment and maintenance of a Undetected errors in the data base or
voucher specimen collection should be programming can be disastrous to
considered for biological data. interpretation. Problems in managing
Transcription errors during data entry the data base can occur if steps are not
can be reduced with double data entry. taken to oversee the data handling,
Table 12-3 gives examples of QC analysis, and summarization. The use
elements for field and laboratory of standardized computer software for
activities. data base management and data
analysis can minimize errors associated
12.3.2 Laboratory Operations with tabulation and statistical analysis.
A final consideration is the possible
The QC elements in laboratory misinterpretation of the findings. These
operations include sorting and potential errors are best controlled by
verification, taxonomy, duplicate qualified staff and adequate training.
processing, archival procedures,
training, and data handling. Potential 12.3.4 Reporting
error sources associated with sample
processing are best controlled by staff QC in reporting includes training, peer
training. Controlling taxonomic error review, and the use of a technical editor
requires well-trained staff with expertise and standard formats. The use of
to verify identifications. Counting error obscure language can often mislead the
and sorting efficiency are usually the reader. Peer review and review by a
most prominent error considerations; technical editor are essential to the
they can be controlled by training and development of a sound scientific
by duplicate processing, sorting, and document.
verification procedures.
Table 12-3 Example QC elements for field and laboratory activities
Project Activity QC Element Evaluation Mechanism
Field Sampling Replicated samples at 10% of Calculate relative percent difference
sites by same field crew. (RPD) of index value or individual metric
score
Replicated samples at one to Calculate RPDs as above; use to
two of total sites by different evaluate consistency and bias.
field crew using same methods.
Physical Habitat Ensure appropriate training and Resume or other documentation of
Assessment experience of operators; experience; discuss and resolve
(Qualitative) multiple observers. differences in interpretation.
Physical Habitat Replicated measurements at Calculate RPDs between replicate
Assessment 10% of sites. measurements; compare to
(Quantitative) preestablished precision objectives.
Laboratory: Sample residue checked for Calculate percent recovery; compare to
Sample Sorting missed specimens to estimate preestablished goals.
sorting efficiency; check
completed by separate lab staff.
Laboratory: Logbook with record of all Not applicable.
Sample sample information.
Tracking
Laboratory: Independent identification Calculate percent error; compare to
Taxonomic and/or verification by specialist; preestablished goals.
Identification ensure appropriate and current
taxonomic literature available;
adequate training and
experience in invertebrate
identifications; reference
collection; exchange selected
samples/specimens between
taxonomists.
Data Proofreading; accuracy of All transcribed data entries compared by
Management transcription. hand to previous form—handwritten raw
data, previously computer-generated
tables, or data reports.
Data Analysis Hand-check of reduced data. For computer-assisted data reduction,
approximately 10% of reduced data
recalculated by hand from raw data to
ensure integrity of computer algorithm.
Appropriate statistics; training. Review by statistician or personnel with
statistical training.

Case Study: Optimization of Benthic Sampling Protocols: gear, mesh size,
replicates
Ferraro et al. (1994) studied the cost-effectiveness of several alternative marine

benthic sampling protocols, including sampling gear, mesh size (0.5-mm or 1.0-
mm), and number of replicates (1-10), in southern California waters. Alternative
sampling gear was:
• 0.1-m2 van Veen grab

• 0.06-m2 van Veen grab
• 0.1-m2 van Veen grab subsampled by 1-6 core samples, 50-300-cm2 total
area subsampled.
Laboratory processing time was recorded for each sampling alternative. Twelve
measures of community structure were examined. Results showed that the power
of detecting differences between sites did not increase greatly for more than 4
replicates. Optimum cost-effectiveness was achieved with 5 core subsamples
(250-cm2 ) of 0.1-m2 grabs, replicated 4 times at each site (Ferraro et al. 1994).
Case Study: Optimization of Benthic Sampling: Seasonal sampling, trend

detection
Alden et al. (1997) examined seasonal and annual trends in estuarine benthic
macroinvertebrates community measures (diversity, total abundance, biomass, %
opportunities). Samples were taken seasonally (4 x per year) from 16 Chesapeake
Bay sites for 9 years. Long-term trends were examined by season, and the power
of detecting trends was examined for alternative sampling frequencies of 1
season, 2 seasons, or 4 seasons per year. Finally, reference and impaired sites
were compared among seasons to determine if some seasons yield greater power
of detection of impairment than other seasons.
Trends in indicator values were apparent and detectable in all seasons. Although
4-season sampling yielded the greatest power of trend detection, it was only
marginally better than 2-season sampling and 1 season sampling. In general,
summer sampling was most sensitive and yielded the greatest power, allowing
detection of trends of 4%-7% change per year in abundance, diversity, and %
opportunist metrics over the 9 year period. Biomass was much more variable: the
minimum detectable trend was approximately 20% change per year for summer-
only sampling (Alden et al. 1997).
Chapter 13
Case Studies
In conjunction with the drafting of this Monitoring Program (PSAMP) as well as

guidance manual, the USEPA Biocriteria for various urban bay, dredge disposal,
Program has also supported or assisted and Superfund action programs. The
in the support of projects around the PSAMP has quantitatively defined
country to evaluate estuarine and population patterns of demersal fishes,
coastal marine survey methods and to but has not defined those patterns for
develop metrics appropriate for use in other demersal fauna such as
different settings. These studies were macroinvertebrates. Nor has any
conducted prior to the creation of this program developed data to explain how
guidance document. Each case study the fauna are responding to the
exemplifies a section within the environmental stresses associated with a
guidance. This chapter summarizes contaminated substrate.
studies conducted in the Pacific
Northwest, Gulf of Mexico, and along 13.1.1 Study Objectives
the Middle and South Atlantic coasts.
The Puget Sound study (Eaton and
Some of the material presented here also Dinnel 1993, Eaton 1994, 1995) was
appears in the body of this text and the initiated in 1993 to document demersal
information which follows expands on populations in their entirety, and to
that discussion. Further, the principal attempt to relate the resulting biological
investigators or other contact in each information to sediment chemistry,
instance are listed with their addresses toxicity, and infauna. The pilot study,
and phone numbers should the reader funded by USEPA, began by assessing
desire to comment or request more the utility of using two different trawls
information. to quantitatively define demersal
populations at a given point in time.
13.1 Puget Sound - Using the resulting documented
Development of Trawl- population patterns and comparisons
between reference and contaminated
Based Tools For the areas, the study objectives were
Assessment of Demersal ultimately to:
Fauna
(Macroinvertebrates and < Gain a greater understanding of how
Fishes): A Puget Sound demersal populations are being
Pilot Study affected by pollution and habitat
degradation;
The relationship between pollution and
the health and status of marine benthos < Determine which patterns reflect
are being studied in the Puget Sound environmental stress;
region of Washington state (Figure 13-1).
Detailed sediment data, including < Develop metrics (biological
information on chemistry, toxicity and measures) which would help to
infaunal populations, are being collected build a biological index for the rapid
for the Puget Sound Ambient
Figure 13-1 Puget
Sound
General
location of the
case studies.
Delaware Bay
- Ocean City
North
Carolina
Indian River
Galveston Bay
Tampa Bay
and economical assessment of stress condition (six miles to the north) in

in subtidal biotic marine Quartermaster Harbor on Vashon
communities. Island. Bottom depth, sediment grain-
size analysis (either historical
13.1.2 Study Methods information or wet-sieving technique for
percent fines), bottom temperature, and
Beam and otter trawls were used to salinity data were recorded for all
sample Puget Sound demersal fauna in stations to insure meaningful pairing of
1993 and 1994. A 3-m beam trawl (with sites.
a “tickler” chain attached in front of the
net) towed at 1.5 knots proved to be Spatial coverage of the study area was
very effective for sampling most determined using a stratified random
demersal invertebrates and small or design. The Hylebos and Blair
juvenile fishes. A 7.6-m Southern Waterways were divided into four
California Coastal Water Research strata, the Thea Foss into three strata,
Project otter trawl, towed at 2.5 knots, and Quartermaster Harbor into two.
was best suited for sampling larger and One station was located in each stratum,
more mobile marine fishes and except in mid-Quartermaster Harbor
invertebrates. All trawl catches were with two stations — one being an
held in tubs of running seawater historical sediment monitoring station.
following capture, and fauna were A second station was placed in the mid-
subsequently sorted, identified, Quartermaster Harbor stratum to
counted, measured and weighed. All compare the variability in results
organisms were released on station. between two stations of close proximity
with similar depth and sediment grain-
In the first year of the pilot study (1993) size.
sampling focused on two of the Tacoma
Waterways, the contaminated Hylebos Evaluation of ten consecutive and seven
Waterway (a Superfund site) and the non-consecutive otter trawl replications
adjacent, less-impacted Blair Waterway. in 1993 led to the conclusion that four or
Sampling in 1994 compared another five otter trawl replications were needed
Tacoma Waterway and Superfund site, to quantitatively define the demersal
Thea Foss (City) Waterway, with a fish community at a given station, and
cleaner and more natural reference that the replications should not recur in
13-2 Case Studies

less than four hours. The 1994 sampling to be very similar in depth, sediment
design incorporated these grain size, bottom temperature and
recommendations, utilizing a sampling salinity. A comparison of catch data for
effort of five otter trawl and three beam the two stations indicated that fish
trawl replications per station. abundance in the reference area was
actually lower compared to that found
The extensive data set resulting from the at the contaminated Superfund site
trawl surveys was entered into (Figure 13-2a), whereas fish biomass was
computer spreadsheets as catch files, significantly greater at the reference site
and was sorted and statistically (Figure 13-2b). This finding indicated
analyzed for patterns and relationships. that the individual fishes at the reference
The null hypothesis for the pilot study site must be considerably larger than
was that the contaminated and non- those found at the contaminated site,
contaminated sites were not and/or that sensitive fish species found
significantly different for the parameters at the reference site but not at the
measured (i.e., fish abundance, biomass, contaminated site tended to be much
mean individual weights, diversity and larger than the other fish. Both factors
evenness). Data comparisons were contributed to the differences. Eight of
tested for statistical significance using the thirteen fish and invertebrate species
either a parametric test (i.e., Student’s common to both sites showed
two-tailed, two-sample t-test either significantly greater mean individual
paired or independent) or a non- weights at the reference stations, and of
parametric test (i.e., two-sample the remaining five, only one species was
Kolmogorov-Smirnov Test) depending consistently larger at the contaminated
on the outcome of the test for normality sites (Figure 13-2c). Also the
(i.e., one-sample Kolmogorov-Smirnov cartilaginous fishes (i.e. spiny dogfish,
normality test). Species diversity was spotted ratfish, and the skates),
calculated using the Shannon-Wiener tentatively classified as sensitive species,
Index (H’) with the natural logarithm, were only rarely encountered in the
although simple species richness contaminated waterways and were very
measurements proved to be more large compared to the bony fishes.
statistically significant. Species
evenness was measured with Pielou’s A preliminary list of tolerant and
evenness index (J) and number of sensitive fish and invertebrate species
species $90% of total abundance. was generated for the Tacoma
Dominance was measured using the waterways and Quartermaster Harbor
dominance ratio, Nmax / N, where Nmax = fauna based on the pilot study results
number of individuals of the most (Table 13-1). Tolerant species were
abundant species, and N is the total defined as those whose relative
catch. abundance at contaminated sites is
significantly greater than or
13.1.3 Study Results indistinguishable from those species
found at comparable reference sites (i.e.,
Pilot study results focused on a site of comparable depth, salinity,
comparison of the reference and dissolved oxygen, sediment grain-size,
contaminated stations which showed slope, and density of structures such as
the best match of environmental eelgrass). Sensitive (intolerant) species,
parameters. Reference station QMH1 in on the other hand, were defined as those
upper Quartermaster Harbor and species whose relative abundance is
contaminated station TF1 in the upper
end of the Thea Foss Waterway proved
Figure 13-2a
Bony fish Bony Fish Abundance and Total Fish Abundance for Reference
abundance (QMH) and Contaminated (TF) Sites
and total fish
abundance for
reference and
contaminated 25.0 OTTER TRAWL
sites.
Abundance per 100 m2

20.0
15.0
P=0.0003
Bony Fish (Osteichthyes)
Abundance
10.0
Bony plus Cartilaginous
P=0.0003
Fish Abundance
5.0
0.0
QMH QMH QMH QMH QMH
TF TF TF TF TF
1.1 1.2 1.3 1.4 1.5
1.1 1.2 1.3 1.4 1.5
REFERENCE CONTAMINATED
Station and Replication
Figure 13-2b
Bony fish Bony Fish Biomass and Total Fish Biomass for Reference (QMH)
biomass and and Contaminated (TF) Sites
total fish
biomass for 3.0
OTTER TRAWL
reference and
contaminated P=0.0001
2.5
sites.
Bony Fish (Osteichtheys)
Biomass per 100 m2
Biomass
2.0
Bony plus Cartilaginous Fish
Biomass
P=0.0001
1.5
1.0
0.5
0.0
QMH QMH QMH QMH QMH TF TF TF TF TF
1.1 1.2 1.3 1.4 1.5 1.1 1.2 1.3 1.4 1.5
REFERENCE
Station and Replication CONTAMINATED
13-4 Case Studies

Figure 13-2c
Mean Individual Weights of Fish Species from Contaminated (TF) and Mean
Reference (QMH) Stations individual
0.40 weights of fish
species from
0.35 contaminated
Average Weight (KG)

Contaminated Stations (TF) NS and reference
0.30
stations.
Reference Stations (QMH)
0.25
0.20
0.15
0.10
NS
0.05
0.00
Shiner Perch
Snake Prickleback
Adult Tomcod
Speckled Sanddab
English Sole
Rock Sole
Starry Flounder
Sand Sole
Pacific Herring
Staghorn Sculpin
significantly greater from a reference indicated that fish species richness was
area than from a comparable notably greater at the reference site (16
contaminated site. species) than at the contaminated station
(11 species). When statistically
The sensitive species index, derived examined on a trawl-by-trawl basis (i.e.,
from the proportion of sensitive species using the mean number of fish species
abundance or biomass to the total of per sample), fish species richness was
sensitive plus tolerant species, was significantly greater at the reference
applied to the pilot study catch data. stations. Fish species evenness, as
Index results showed significant measured by the number of fish species
differences for all comparisons (i.e., fish 90% of total abundance, was also
abundance and biomass, and fish plus significantly higher at the reference
invertebrate abundance and biomass stations, both when paired with the
between contaminated and reference Thea Foss stations, and when compared
sites). The results suggested that such as a whole. External abnormalities or
an index, if tested independently for anomalies, such as fin erosion or skin
annual and seasonal variation, could be tumors, were extremely rare at all
very useful in tracking recovery of an stations during both study years,
area after cleanup or remediation, or to thereby suggesting that it may not be a
help classify impacted sites relative to useful indicator of environmental stress.
the benchmarks established through the
biocriteria. The results of the first year of sampling
indicated that raw or averaged
Pilot study results also indicated that abundance data were not useful in
fish species richness and fish species differentiating contaminated and
evenness were useful measurements in reference sites. This discovery led to an
the site discrimination process. increased effort in recording biomass
data during the second study year, and
Although no difference was found in to the inclusion of a more natural
species richness using the beam trawl reference condition. Results of the
sampling method, otter trawl catches second year of sampling emphasized the
Table 13-1. A preliminary list of tolerant and sensitive fish and invertebrate species from the Tacoma
Waterways and Quartermaster Harbor.
FISH
Tolerant Species Sensitive Species
English sole Spiny dogfish

Sa nd sole Spotted ratfish
Fla the ad sole Lon gno se s kate
Pacific tomcod Rock s ole
Shiner surfperch Starry flounder
Snake prickleback Speckled sanddab
Pa cific stag horn sculpin Pile surfperch
Striped surfperch
Bay goby
Blackbelly eelpout
Bay pipefish
Plainfin midshipman
INVERTEBRATE
Panda lus da nae : coonstripe shrim p Cu cum aria m iniata: sea cucumber
Crangon spp.: sa nd shrim p Cu cum aria piperata: spotted sea
cucumber
Cancer gracilis: purple cancer crab Pentam era populifera: crescent sea
cucumber
Cancer productus: red rock crab Parastichopus californica: edible sea
cucumber
Cancer magister: Dungeness crab Solaster stimpsoni: sunstar
Lophopanopeus bellus: crab Pagurus spp.: hermit crabs
Ev asterias trosc helli: mottled seastar Nassarius mendicus: sn ail
Me tridium senile: plume anem one
ecologically important fact that the any future ecologically-based indexes of

reference sites, despite fewer or equal pollution. Candidate attributes of
numbers of fishes, supported more than demersal fauna which warrant further
twice the fish biomass than the study are listed in Table 13-2.
contaminated site. Almost every fish
species common to both areas was Primary Contact: Charles Eaton
significantly larger, and fish species Bio-Marine Sciences
richness and evenness were significantly 2717 3rd Ave. N
higher at the reference site. Seattle, WA 98109
206-282-4945
The sensitive species index proved to be
useful in differentiating sites. The
identification of sensitive (intolerant)
and tolerant demersal marine species is
in its infancy, due in part to the paucity
of data on demersal marine
communities and the lack of
quantitative sampling methods. With
the development of these sampling
techniques, the pilot study
demonstrated that information on the
demersal fauna should be included in
13-6 Case Studies

Table 13-2. Candidate attributes of demersal fauna showing significant differences in the present study.
Candidate Metrics Preliminary Range of Values (and Range of Values (and
Expectation mean) from Present mean) from Present
from Present Pilot Study: IMPAIRED Pilot Study:
Study: SITE: Thea Foss Wty. REFERENCE SITE:
IMPAIRED SITE QM Hbr.
Total Fish Abundance per Elevated or no TF 1: 20.6 to 22.7 QMH 1:
100 m2, 4-6 m. Depth. difference mean = 21.4 8.3 to 14.2
(10-15 m.—no difference). mean = 11.9
Total Fish Biomass per 100 Reduced 0.54 to 0.97 kg (mean = 0.81 to 4.82 kg (mean =
m2 0.73) 2.64)
Fish Species Richness Reduced per tow: 6-13 per tow: 11-18
(Number of fish species) cumulative:10-14 cumulative:15-18
Fish Species Evenness Reduced 3-6 (mean = 3.7) 4-7 (mean = 5.2)
(Number of Fish Species $
90% of Total Abundance)
Mean Individual Weight Reduced e.g. English Sole 45 to e.g. English Sole 125 to
and Size of all Species 114 g (mean = 75 g.) 484 g. (mean=204 g.)
(except Pacific Herring and
Staghorn Sculpin)
Tolerant Species Elevated or (in e.g. English Sole e.g. English Sole 0.2 to
Abundance and Biomass some cases) no 2.8-10.1 (5.3) per 100 m2 6.1 (2.3) per 100 m2
(English Sole, Pacific difference e.g. juv. Tomcod e.g. juv. Tomcod 0 to
Staghorn Sculpin, Pacific 0.39 to 9.87 (7.3) 0.69 (0.4)
Tomcod, Shiner Surfperch, e.g. Purple Crab e.g. Purple Crab 0.0 to
Snake Prickleback, Purple 4.7 to 56.0 (22.8) 6.3 (2.7)
Crab, Mottled Seastar, Plum
Anemone)
Sensitive Species Reduced e.g. Bay Goby 0.4 to 3.9 e.g. Bay Goby 28.6-
Abundance and Biomass (1.7) per 100 m2 41.9 (36.5) per 100 m2
(Bay Goby, Starry Flounder, e.g. Cucumaria piperata e.g. Cucumaria piperata
Rock Sole, Cartilaginous Zero 0.0 to 5.9 (2.5)
Fish, Sea Cucumbers)
Sensitive Species Index Reduced 0.016 to 0.098 mean = 0.075 to 0.787 mean =
(proportion of sensitive to 0.049 0.357
sensitive + tolerant)
13-8 Case Studies
13.2 Galveston Bay - upper portions. Oyster Bayou,
Dickinson Bayou, Texas City Hurricane
Development of a Canal, Highland Bayou Diversionary
Rapid Bioassessment Canal, and Cedar Lakes Creek were
Method and Index of selected to fulfill these criteria. Oyster
Biotic Integrity For Bayou is a minimally impaired coastal
bayou located in the middle portion of
Coastal Environments: Galveston Bay and flowing south to East
Northwestern Gulf of Bay. Oyster Bayou stations were
Mexico Pilot Studies characterized by a silty clay substrate.
The moderately impaired Dickinson
13.2.1 Study Objectives Bayou is located in the northeastern
portion of Galveston County. Dickinson
A study was conducted on selected Bayou is characterized by sandy to silty
streams and bayous within Galveston clay substrates and is impaired by both
Bay, Texas (Figure 13-1) coastal point and nonpoint sources. The Texas
ecosystems, in order to characterize the City Hurricane Canal is an industrial
expected fish assemblages of various canal that flows into the Texas City ship
types of waterbodies (with varying channel, and receives industrial and
water and habitat quality) (Guillen stormwater discharges. The majority of
1995a). A second study objective was to the canal banks possess a steep slope,
develop a prototype rapid and little bank vegetation, and the
bioassessment technique similar to the southern shoreline is an artificial levee.
Index of Biotic Integrity for the The Highland Bayou Diversionary
northwestern Gulf of Mexico. In order Canal is an artificial waterbody created
to meet the second objective, several by the Army Corps of Engineers in 1983.
criteria for the development of the The canal was created by channelization
method had to be met. First, the method of the upper reach of Highland Bayou
had to be ecologically relevant, that is proper and construction of an earthen
any metric or ranking system had to dam directly below the channelized
directly relate to ecological function and portion, in order to reroute water
structure. Secondly, the method had to through a dredged canal into Jones Bay.
be taxonomically simple or kept to the The canal is tidally influenced and
broadest taxonomic/functional group of receives effluent discharge from
organisms that provide the most municipal wastewater treatment plants
information. The methods also had to and runoff from surrounding
be simple (in terms of equipment, labor, agricultural grazing and pasture lands.
and analysis) cost effective, easily Cedar Lake Creek is a minimally
standardized, subject to easy replication, impaired rural bayou which extends 24-
and adaptable to a variety of miles from its origin at the intersection
environments. of Cedar Lakes to the Gulf Intracoastal
Canal. There are no active discharges in
13.2.2 Study Methods the watershed, however, an oilfield is
present at its upper reaches.
The sampling design consisted of five Predominant land use in the area is
bayous classified according to the cattle grazing and the San Bernard
potential for anthropogenic impact; i.e., Wildlife Refuge.
urban versus rural, impaired versus
unimpaired and salinity effects; i.e., To summarize, two minimally impaired
lower portions of tributaries versus bayous (Oyster Bayou and Cedar Lakes
Creek) and three impaired waterbodies tool for investigators to evaluate the
(Highland Bayou Diversionary Canal, relative influence of physicochemical
Texas City Hurricane Canal and variables on coastal nekton
Dickinson Bayou) were surveyed during communities. Survey results showed
the study period. The impaired sites that the majority of water quality
included two that were influenced by variables were within previously
residential and municipal wastewater, documented tolerance limits of estuarine
and one effected by industrial effluent. fish.
Two of the waterbodies were highly
channelized and/or man-made. Site Nekton (fish and macrocrustacea) were
investigations involved seasonal collected using experimental gillnets,
quarterly surveys made at all stations trawls, and seines. Gillnets were 200 x
within each watershed. Sampling was 8-ft experimental monofilament nets
conducted during summer, fall, and with eight panels of varying mesh sizes
winter 1991; spring and summer 1992; (0.5-4-in mesh). Seine collections (five
and winter, spring, summer, and fall replicates of 25-ft hauls) were made
1993. using a 15 x 4-ft common minnow seine
with 1/8-in square mesh nylon netting.
In order to evaluate the relationship Trawls were made at main channel
between water quality and fish stations in each watershed, using a 10-ft
communities, various hydrological, otter trawl with 1-in mesh in the wings
habitat, and biological data were and 1/4-in mesh in the cod end. Four
collected concurrently. Qualitative replicate trawls (five minute tows, each)
habitat measurements including were made at each of the mainstream
primary and secondary tributary depth, stations. Nekton collected via all
width, substrate type, and shoreline sampling methods were identified to the
vegetation were noted at each station. A lowest possible taxon, enumerated, and
rapid field method for the evaluation of measured.
percent sand in sediments was also used
to evaluate effects of sediment size on 13.2.3 Study Results
nekton populations. Measurements of
surface and bottom temperature, Several biological metrics were
dissolved oxygen, conductivity, salinity considered during the pilot study based
and pH were made. Surface water on historical usage and recent
samples were also collected for the recommendations in the literature.
determination of total organic carbon, Community metrics generated from
fecal coliforms, total and pilot study data included: total catch,
orthophosphate, nitrates, total ammonia, log-transformed total catch, number of
total suspended solids, and chlorophyll nekton taxa, Shannon-Wiener diversity
a. Individual water chemistry and index, Pielou evenness index, total
habitat values were plotted against number of taxa making up 90% of the
seasons and stations to evaluate catch, dominance ratio (ratio of most
temporal and spatial patterns. abundant species/total catch), number
of crustacean species; number of
In addition, Pearson's correlation "bottom taxa"; i.e., sciaenids, flatfish,
coefficients and stepwise and direct blue catfish; number of predatory
discriminant analyses were used to species; number of "minnow" taxa; i.e.,
determine the relationship between the Poeciliids and/or cyprinodonts; number
variables and clustered groupings of of goby taxa; proportion of total catch as
stations. The analyses provided another bay anchovy; proportion of total catch as
13-10 Case Studies

"shad"; i.e., clupeids and engraulids, difficult to compare metrics derived
proportion of total catch as poeciliids; from the pilot study with other studies.
proportion of total catch as Penaeid Pilot study results indicated that it
shrimp; and proportion of total catch as seems feasible that a prototype estuarine
palaemonid shrimp; i.e., grass shrimp. bioassessment system based on nekton
The rationale for each proposed metric is community collections can be used to
provided in Table 13-3. successfully document impacts from
pollution. Analysis of potential metrics
Trawl, seine, and gillnet results were through discriminant analysis, graphical
utilized in a cluster analysis, and then evaluation of cumulative distribution,
subjected to stepwise discriminant frequencies and correlation analyses
analyses. Observed seasonal and spatial yielded the proposed metrics listed in
patterns and/or temperature and Tables 13-4, 13-5 and 13-6. The
salinity related correlations were used to categories utilized in the framework of
determine whether seasonal or salinity- the proposed system were based on the
adjusted metrics were needed. In following protocol. Depending on the
addition, the decision to include data metric, those values less than the 15th
from "impaired" sites in the derivation percentile were categorized as "concern".
of metrics was also evaluated using The interquartile values; i.e., 15-85th
these analyses. If initial statistical percentile were categorized as "normal",
analyses failed to show differences and values exceeding the 85th percentile
between the reference sites and were classified as "excellent". In some
impaired sites, then all sites were pooled cases where high metric values denoted
for derivation of metrics. degraded conditions, the inverse of the
proposed scheme was used; i.e., ‹15th
Due to the strong seasonal and/or percentile = "excellent". The
spatial trends observed in various classification system was based
metrics using the seine data, cumulative primarily on statistical distributions of
percent distributions of each candidate the observed data. Where data was
metric were calculated by season for insufficient, a "not recommended"
minimally impaired watersheds. disclaimer was listed.
Results of the distributions are
presented in Table 13-4. Metrics were It was difficult to single out one water
adjusted where distributions indicated quality variable as having the most
truncated values using the following influence on community structure and
approach. If the distribution line could the proposed metrics. Therefore, a
be extended to the 15th or 85th percentile conservative approach was taken by
value without crossing the Y axis, then grouping by season and utilizing all
that estimated value was used. If it data across various salinity levels.
could not, the metric was not used
during that season and/or the metric The proposed Index of Biotic Integrity
rating was adjusted to reflect only two (IBI) metrics derived from the pilot
conditions (e.g., normal and excellent). study would be most confidently
This same procedure was used to derive applied to situations where salinities
a proposed metric system using trawl range from 1-25-ppt. Continued
data (Table 13-5). A proposed list of calibration of this system with
prototype metrics using gillnet catch additional data sets is needed. The
data was developed (Table 13-6); proposed metrics need to be evaluated
however, since gillnet design and against independent data sets including
deployment is variable, it may be those in high (>25-ppt) salinity regimes.
Table 13-3. Rationale for the inclusion of proposed nekton community metrics.
Metric Rationale
Total Catch Total abundance is a rough measure of the total community
population and as such gives no information on individual species
population levels. Low abundances can be caused by various
stressors. It should be noted that high abundances caused by
individual opportunistic species can also indicate a disturbed
community.
Log Total Catch Due to the inherent variability of populations, the patchiness of fish
schools and previously observed distributions of fish, many
ecologists feel that the log-normal distribution fits the distribution of
nekton populations better. Therefore log total catch may be a more
appropriate indicator of total population levels. In order to handle
zero catches, however, a log (catch + 1) transformation is needed.
Total Number of Nekton Taxa The species richness of any community is extremely important.
Reductions in species number may indicate an overall reduction in
available habitat or the presence of environmental stressors. This
may be due to the avoidance or death of sensitive species in an
area. The number of taxa collected is a relatively economical
measure. On a relative scale it is the cheapest information
obtainable from catch data.
Cumulative Number of The cumulative number of taxa is somewhat different than the total
Nekton Taxa number of taxa in that it reflects the upper limit of the number of
taxa one would expect to collect within a single replicate sample.
Large discrepancies between mean and cumulative number of
species may indicate high variability in habitat or distribution of
species. Like the total number of taxa metric a low cumulative
number of taxa can reflect limited habitat and/or the presence of
environmental stressors.
Total Number of Fish Taxa This metric is closely related to total nekton species numbers.
However, it was added to address situations where only fish data is
tabulated.
Nekton Species Diversity The Shannon-Wiener diversity function was selected to evaluate
nekton communities. This commonly used function (H') was
developed to incorporate the two most important components of
diversity, namely richness and evenness. Species richness is
normally tabulated. However, species richness alone provides no
information on how evenly individuals are distributed among
species. The majority of communities studied by ecologists show a
log-normal pattern of species abundance in which a relatively few
species possess a rather large number of individuals and a rather
large number of species possess few numbers of individuals. A
diverse community is one in which species number and evenness
are maximized. One problem with the use of H' is the fact that
various combinations of species numbers and evenness can yield
the same answer. Therefore diversity indexes should only be
evaluated in the presence of species richness and evenness.
13-12 Case Studies

Table 13-3 (Cont’d). Rationale for the inclusion of proposed nekton community metrics.
METRIC RATIONALE
Nekton Evenness One factor that influences diversity directly is the evenness of the
distribution of organisms between species. Populations possessing
high numbers of taxa but with highly uneven distributions between
taxa (e.g. highly dominant taxa) may reflect underlying habitat
limitations, stressors or seasonal patterns. One of the most
popular indexes used by marine biologists is the Pielou's evenness
index (J). This index is defined as:
J = H'/ln(S),
where H' is the Shannon-Weiner index,
ln is the log base (e)
and S is equal to number of taxa
This index expresses H' relative to the maximum value that H' can
obtain when all of the species in the sample are perfectly even with
one individual per species.
Number of Nekton Taxa = This index is the number of taxa that together add up to at least or
90% Catch exceed 90% of the total catch. This is another measure of
evenness. High values would indicate a community in which there
is no clear dominant taxa. This index is influenced by the same
factors which effect the evenness index.
Nekton Dominance Ratio This has also been referred to as the Berger-Parker index. This is
the ratio Nmax /N, where Nmax = number of individuals present in the
most abundant taxa, and N is the total catch. This equation is
computationally simple and can be easily programmed into
spreadsheets. In addition, it is intuitively easy to understand. High
dominance reactions reflects dominance of the community by a few
individuals which relates to an uneven distribution of individuals
within taxa resulting in poor diversity. This may be related to
potential stressors and other factors cited under the discussion of
Pielou's evenness.
Number of Crustacean The number of crustacean taxa present in the nekton is largely a
Nekton Taxa function of 4 principle groups. The first group are crab species
including blue crab, Callinectes sapidus. The second group
includes seasonally dominant groups of Penaeid shrimp which
migrate into tidal creeks and bayous as postlarva and juveniles.
The third group includes resident species of grass shrimp, genus
Palaemonetes. The final group include freshwater prawns, genus
Macrobrachium, and crayfish genus Procambarus. The presence
of crustacean taxa indicates a healthy population of benthic
herbivores and omnivores which serve as the primary food source
for many estuarine fish. In addition, crustaceans are especially
sensitive to organic pesticides.
Number of Predatory Fish Predatory fish were defined as fish in the family Carangidae,
Taxa Scombridae, and the genera Paralichthys, Lepisosteus,
Micropterus, Cynoscion, Morone and the species Sciaenops
ocellatus, Synodus foetens and Elops saurus. These species
represent individuals at the top of the food chain. Impacts to other
species they depend on may reduce these predators indirectly. In
addition, through the process of biomagnification predators are
more likely to bioconcentrate high levels of pollutants found in the
lower portions of the food chain.
Table 13-3 (Cont’d). Rationale for the inclusion of proposed nekton community metrics.
METRIC RATIONALE
Number of "Minnow" Taxa The number of "minnow" taxa include resident species of
Cyprinodontidae and Poeciliidae. These two groups of small fish
represent the majority of resident species inhabiting marsh and
shallow water environments. The majority of these species are not
normally found offshore or in deeper waters due to predation. A
high number of these taxa may reflect habitat suitability of a
particular location to resistant species. Since these species are
largely non-migratory, their presence or lack of may indicate long-
term environmental perturbation. In contrast, high populations of
these species may correlate the absence of larger predators and/or
the presence of marginal habitat unsuitable for other less tolerant
taxa.
Number of Goby Taxa This is another group of resident taxa that are primarily carnivorous,
feeding on small invertebrates. In addition, gobies are extremely
territorial and tend to stay within a defined area. Most gobies are
benthic. Reduced numbers of gobies would indicate localized
impacts to habitat, water quality and secondary impacts on food
sources namely, epibenthic invertebrates.
Proportion of Nekton Catch Poeciliids are a group of fish that are generally extremely tolerant to
as Poeciliids poor water quality. Notable examples include the mosquitofish
(Gambusia affinis) and molly (Poecilia latipinna). These two
species are often found in harsh habitats where few other species
live. In addition, they are typically found in areas (e.g., shallow
flats) which are difficult for predators to exploit. A predominance of
Poeciliids in shoreline communities can therefore indicate degraded
conditions and/or lack of predators.
Proportion of Nekton Catch One of the most important species ecologically and commercially
as Penaeid Shrimp are the Penaeid shrimp, including the estuarine white shrimp
Penaeus setiferus, the brown shrimp P. aztecus, and the less
abundant pink shrimp P. duorarum. Typically these species enter
the estuaries as postlarvae. With continued migration they reach
tidal creeks and bayous as juveniles and spend the early part of the
first year in these areas prior to migrating back to the ocean to
spawn.
The proportion of catch as Penaeid shrimp may be an excellent

ecological indicator. Penaeid shrimp can serve as a metric that
addresses the nursery functions of a waterbody. It is also a lower
food chain omnivore. Many species are dependent upon this
invertebrate for food. Therefore, reduced numbers of shrimp can
detrimentally effect the entire nekton community. In addition, since
it is an arthropod it may serve as an excellent indicator of
secondary impacts associated with pesticide use.
13-14 Case Studies

Table 13-4. Proposed seine metrics for use in an estuarine IBI along Texas coast.
Metric Summer Fall Winter Spring Score
Value Value Value Value
Category A
(A) Total Catch <200 <50 NA NA 1
200-450 50-400 900 700 2
>450 >400 >900 >700 3
*(A) Log Catch <.5 <.9 <4.2 <1.5 1
4.5-6.0 3.9-5.8 4.2-6.4 1.5-6.3 2
6.0 5.8 >6.4 >6.3 3
*Prop. Pen. Shrimp <.01 <25 NA NA 1
0.01-0.3 .25-.56 NA 0.04 2
>0.3 >56 NA >0.04 3
Category B
(B) Prop. Shad >0.83 >.60 >.59 >.78 1
NA .04-.60 NA NA 2
0.83 0.04 .59 .78 3
*(B) Prop. B. Anchovy >0.8 >.52 >.13 >.34 1
If Bay A. = 0 NA .04-.52 NA NA 2
then use 'Shad' metric 0.8 <.04 .13 .34 3
*Dominance Ratio >0.88 >.65 >.82 >.78 1
0.44-0.88 .40-.65 .26-.82 .27-.78 2
<0.44 <.40 .26 <.27 3
Category C
*(C) Mean #Taxa <6 <6 <6 <5 1
6-11 6-10 6-10 5-10 2
>11 >10 >10 >10 3
(C) Cum. #Taxa <10 <6 <11 <11 1
10-19 6-11 11-18 11-19 2
>19 >11 >18 >19 3
(C) Mean #Fish Taxa <3 <3 <3.5 <4 1
3-7 3-7 3.5-7 4-8 2
>7 >7 >7 >8 3
Total IBI Score
Concern 5-7 5-7 4-5 7-9
Normal 8-12 8-12 6-10 10-12
Excellent 13-15 13-15 11-12 13-15
Total IBI Score (WHEN INVERTS NOT USED)
Concern 4-5 4-5 4-5 5-6
Normal 6-10 6-10 6-10 7-10
Excellent 11-12 11-12 11-12 11-12
* Recommended metric; if mean log total catch or total catch = 0, then score = high concern.
Table 13-5. Proposed trawl metrics for use in an estuarine IBI along Texas coast.
Metric Summer Value Fall Value Winter Spring Score

Value Value
*Prop. Total Catch * <0.42 * * 1

as P. Shrimp # 0.45 .42- .83 * # 0.08 2
>0.45 >0.83 * >0.08 3
*Prop Total Catch >0.06 >0.08 * >0.03 1

as Shad * * * NA 2
# 0.06 # 0.08 * # 0.03 3
Category A
*Mean # Nekton <1.8 <4.3 <4.4 <4.1 1

Taxa 1.8-9.3 4.3-9.9 4.4-8.8 4.1-7.7 2
>9.3 >9.9 >8.8 >7.7 3
Mean # Fish Taxa <2.2 <4.2 <2.1 <1.6 1

2.2-6.3 4.2-6.6 2.1-6.8 1.6-4.9 2
>6.3 >6.6 >6.8 >4.9 3
Total IBI Score
Concern 4 3 1 4
Normal 5-8 4-8 2 5-8
Excellent 9 9 3 9
NOTE: To avoid problems caused by division by zero use the following formulas: For shrimp and shad
proportions let metric value = taxa group catch/(total catch + 1). Alternately if any one replicate total
catch = 0, then an IBI score of 'concern' can be given.
NOTE: Avoidance of winter sampling is recommended due to lack of suitable metrics.
* Recommended metric; if mean log total catch or total catch = 0, then score = high
concern.
13-16 Case Studies

Table 13-6. Proposed gillnet metrics for use in estuarine IBI along Texas coast.
M etric Assign ed M etric Score
0 1 2 3
1) Total Nekton Catch 0 1<26 26<47 $47
2) Category 2 (Pick 1 of the 2 Metrics Listed)
2a) Num ber of 0 1<7 7<8 $8
Nekton Taxa
2b) H' * <1.25 1.25<1.85 $1.85
3) Category 3 (Pick 1 of the 2 metrics listed)
3a) Evenness J * <.58 .58<.81 $.81
3b) Num ber of Taxa * <4 4<6 $6
= 90% Total
Nekton Catch
No. Crust. Spp. * N ot R ecom . Not N ot R ecom .
R ecom .
4) No. Pred. Taxa * 0 1 >1
No. "Minnow" Taxa * N ot R ecom . Not N ot R ecom .
R ecom .
5) No . Sca enids/B. C at. * 0 1-2 >2
Taxa
Total IBI Score (SUM OF 0 5-6 7-13 14-15
ALL 5 M ET RIC
CATEGO RIES)
Total IBI Rank HIGH CONCERN NORM AL EXCELLENT
CONCERN
Due to the lack of strong correlation of the index. Proposed FHI values for
between the seine and trawl-derived Gulf Coast bioassessments are listed
metrics, it is advisable that future in Table 13-7. The FHI proved to be
studies use both gear types. Since time and cost efficient, and yielded
gillnet derived metrics were least information that was complementary
sensitive to water quality fluctuation, to the IBI.
and gillnet use is labor intensive and
difficult to replicate, gillnetting is the
least favored approach for evaluating
nekton community health.
A fish health index (FHI) was tested

during the pilot study to evaluate its
utility in assessing impacts on
estuarine fish communities. The FHI
methods mirrored those used by the
Tennessee Valley Authority (Dycus
and Meinert 1993, Dycus 1995).
Further evaluation is needed to
determine the discriminatory power;
i.e., impaired versus unimpaired sites
Table 13-7. Proposed fish health index and condition factors for use in estuarine rapid
bioassessments of Texas Gulf coast tidal tributaries.
FISH HEALTH INDEX
Assigned FHI Rank
Species 1 2 3
Blue Catfish FH I Score >70 40-70 <40
Atlantic Croaker FHI >50 30-50 <30

Score
Sea Catfish "Hardhead" >30 * #30

(least recom m end) sco re
Spot FH I Score >61 32-61 <32
AVERAGE SPECIES FHI 1-1.4 1.5-2 .5 $2.6

RANK
Total FHI Rank based on CONCERN NORM AL EXCELLENT

average scores of single
species
CONDITION FACTOR
Assigned Condition Factor (CF) Rank
Species 1 2 3
Blue Catfish CF <.78 .78-.97 >.97
Atlantic Croaker CF <1.02 1.02-1.15 >1.15
See Catfish "Hardhead" <.82 .82-1.10 >1.10

CF
Spot CF <1.25 1.25-1.44 >1.44
AVERAGE SPECIES CF 1-1.4 1.5-2 .5 $2.6

RANK
Total CF Rank based on CONCERN NORM AL EXCELLENT

average scores of single
species.
13-18 Case Studies

The application of estuarine rapid
bioassessment techniques in studies of
Gulf of Mexico coastal environments
is warranted, based on results of the
pilot study. Several of the methods
tested in the study (including seine
and trawl based IBI and FHI) would
aid water quality and fisheries
scientists in their evaluation of water
and habitat quality impacts resulting
from human activity. The pilot
bioassessment methods meet the
requirements for inclusion in routine
monitoring programs including: low
cost, low effort, readily obtainable
equipment, relatively easy taxonomy,
and replication of effort which is
suitable for statistical analyses.
Primary Contact: George J. Guillen,

U.S. Fish & Wildlife Service
1655 Heindon Rd.
Arcata, CA 95521
707-825-5109
[email protected]
13-20 Case Studies
13.3 Tampa Bay - macroinvertebrates. This process was
Development of a consistent with Florida's biological
integrity standard as defined in the
Community-Based Metric Florida Administrative Code. After the
for Marine Benthos: A ponar samples were collected,
Tampa Bay Pilot Study macroinvertebrates were also sampled
at each location using a modified Renfro
13.3.1 Study Objectives Beam Trawl towed for a distance of 4-m.
State biological criteria in Florida have The Renfro Beam Trawl is a conical net,
been set at a 25% decrease in Shannon- open at the large end, which is normally
Wiener diversity of benthic communities towed over the surface of the substrate.
in test versus reference sites. Input data The net is maintained in an open
have been the sum of three ponar grab position by attaching it to a rigid pole or
samples per site; however, evidence has beam. The body of the net is
suggested that these methods and constructed of nylon bolting cloth (50
criteria are not sensitive enough. Pilot openings/cm2 , which tapers to a
studies in the Tampa Bay area (Figure plankton net fitted with a removable
13-1) have tested a process of classifying bucket. The effective swath width of the
organisms according to their sensitivity custom trawl used for the pilot study
or tolerance to pollution, and was 1.25-m. By towing the net over a
developing an index (the Farrell uniform measured distance, the results
Epifaunal Index) value for test and were comparative (semiqualitative) and
reference sites (Farrell 1993a). The pilot relative abundances of the various
study used biological data from areas species were maintained. The
surrounding treatment plant outfalls in standardized tow length of 4-m
the index calculations, in order to detect effectively sampled approximately 5-m2
differences between test and reference of bottom. Some advantages and
sites that were not evident using the disadvantages of using the epibenthic
state criterion of a 25% decrease in beam trawl are listed in Table 13-8.
diversity.
In advocating the use of the beam trawl,
13.3.2 Study Methods which predominantly samples the
epifaunal and facultative infaunal
Water quality and benthic data were communities, one basic assumption was
developed from a 1992 short-term study made. Provided that the recruitment
of the effects of three small package potential for the individual community
plants on the seagrass communities at components existed, it was assumed that
Fort Desoto Park in Tampa Bay, Florida. within a given set of natural
Three control stations were located on environmental parameters an expected
Joe Island on the southern shore of community of organisms would inhabit
Tampa Bay, and an additional station any predetermined environmental
was located on a small island adjacent to segment. In estuaries and many other
Fort Desoto (that was presumably under marine environments, populations of
the potential influence of the farfield different species vary significantly over
effects). Two sampling sites were the seasons and from year to year;
located at each station, one on the however, these variations follow
shoreline (end of pipe) and a second 50- predictable patterns. In Florida,
m offshore. Four petite ponar replicates numerical dominance may vary among
were collected at each site; however, annual cycles; however, species
only three were analyzed for
Table 13-8. Advantages and disadvantages to using the epibenthic Renfro beam trawl for the
sampling of benthos.
ADVANTAGES DISADVANTAGES
• The epibenthic assem blage is very • Th e m etho d is restricted to level botto m s.

sensitive to anth ropogenic Hard substrates cobble, and emergent
stressors, and this method can be vegetation tend to invalidate the method.
used in both a nearfield and farfield
conte xt w ith equal fa cility. • In areas of abundant seagrasses or
macroalgae beds, sample bulk can be a
• Since this method is limited to level hindrance and some rough field sorting
bottoms, the total number of may be required.
comm on species will be limited
(thereby greatly sim plifying training). • The epifauna tend to be seasonally
[NOTE: T im e re quired fo r an alysis abundant; therefore, this fac tor would
of three ponar samples was have to be calibrated into the m eth od if
approximately 20-hours, whereas m ulti-season al sam pling events are
the time required to analyze a pilot utilized.
study trawl sample was a little less
than 10-h ours ].
• Th is m etho d lend s itself to

subsampling which will reduce
proc ess ing ho urs and increase cos t-
effectiveness.
• Once initial training is completed,

field effo rts can be re latively ra pid
and analytical time can be reduced.
• Sa m ples can be sorted qualitatively,

and a nonparametric analysis can
be applied to provide a method of
quick screening.
composition generally remains stable. The epifaunal and facultative infaunal

Benthic macroinvertebrates, in terms of community was targeted for the pilot
both density and diversity, reach their study since components of the
peak in Florida during the late winter to community appear to be both persistent
early spring (or earlier in the southern and very sensitive to environmental
part of the state). Population minima for stress. Within estuaries and adjacent
most species occur during the summer near-shore areas, physiochemical
months. While they are dramatic, these parameters (e.g., temperature, salinity,
seasonal cycles can be factored into dissolved oxygen) will vary significantly
efforts to establish biocriteria. It is over an annual cycle. Sessile and
important to consider seasonality relatively immobile organisms
because the species which are most (including most of the infaunal
sensitive to environmental stress are components) have evolved either
those which tend to reach their mechanisms which allow them to
population peaks during periods when tolerate these varying conditions, or
water quality factors are both stable and breeding cycles which allow them to
optimal. avoid periods of high stress. The more
motile members of the community
(including the epifauna and facultative
13-22 Case Studies

infauna) have the option of avoidance. sensitivity to toxic substances was taken
During periods of stress, these into account; however, the dominant
organisms can move to deeper water or factor for most of the species was the
to other areas where stressors are relative sensitivity to dissolved oxygen
mollified, and then return when depression. As a result, the Farrell
conditions improve. When an area is Epifaunal Index was probably most
being affected by relatively low levels of sensitive to organic pollution and
anthropogenic stress, only the most eutrophication with associated wide
sensitive members of the benthic swings in dissolved oxygen.
community will respond, and these are
found among the epifaunal and The tolerance criteria for the index in
facultative infaunal components. It is terms of dissolved oxygen requirements
apparent that a method which is truly were as follows:
sensitive to low levels of pollution must
target these components of the benthic 0 Insufficient data to make an
community, thereby advocating their evaluation.
use in the Tampa Bay pilot study. 1 Very tolerant. The identified
species can withstand short
13.3.3 Study Results periods of anoxia.
2 Tolerant. The identified
A bioassessment approach should be species can withstand brief
able to not only detect low levels of excursions to 1.0-1.5 mgL-1 .
environmental stress, but it should also 3 Slightly tolerant - slightly
be able to detect those stress factors at sensitive. The identified
the earliest possible stages. One species can withstand brief
approach which has been used excursions to 2.5-3.0 mgL-1 .
successfully in freshwater environments 4 Sensitive. The identified
has involved the assignment of the species can withstand brief
specific index values to various periods below 4.0 mgL-1 .
community components; i.e., species, 5 Very sensitive. The identified
and basing community assessment on species are basically intolerant
the mean index value derived from of concentrations below 5.0
sampling that community (Lenat 1993). mgL-1 ; however, some species
The Farrell Epifaunal Index proposed in may tolerate brief excursions
the Tampa Bay pilot study was below this provided no other
specifically developed for the west coast stress factors are involved.
of Florida, but it should be useful in
adjacent areas. The index values When the components from a sample
represented a somewhat subjective had been identified, the predetermined
evaluation of the relative tolerance or tolerance values were assigned to the
intolerance to environmental stress. The various species, and a sample Farrell
values were taken from an ongoing Epifaunal Index value was calculated
effort to assign tolerance values to all using the formula:
marine and estuarine
macroinvertebrates identified from the
coast of Florida. Information sources
have included agency monitoring data,
published records, gray literature, and where: ni = number of individuals of
anecdotal information. Wherever species i;
possible, all potential stressors including Ii = tolerance value for species i;
N = total individuals from all sample. Taxa with a value of zero were
species used in the calculation. omitted from calculations. Pilot study
results (Table 13-9) indicated that the
In a strictly qualitative approach, an index had been successful at detecting
index value may be calculated using the differences between test and reference
formula: sites. The resulting Farrell Epifaunal
Index will not meet all needs, and is not
the only metric that could be applied to
beam trawl or similar samples; however,
pilot study results indicate that at a
where: Is = index value for component minimum it should prove to be an
species s; effective screening method.
Ns = number of species used in
the calculation. Primary Contact: Steven Kent, FLDEP,
3319 Maguire Blvd.
Pilot study calculations of Farrell Orlando, FL 32803
Epifaunal Index values required that the 407-894-7555, ext. 2227
appropriate tolerance value (0-5) be [email protected]
assigned to individual taxa in each
sample. The values were then added,
and the summation was divided by the
total number of taxa utilized from the
Table 13-9. Farrell epifaunal index results for the Fort Desoto Park - Tampa Bay Pilot Study.
BEAM TRAWL SAMPLE RESULTS
Sources Controls
Stations 4 6 5 7 2 1 3
Num ber of Taxa 8 13 16 29 27 31 38
Index Total 15 27 35 69 72 84 106
Index 1.88 2.08 2.19 2.38 2.67 2.71 2.79
13-24 Case Studies

13.4 North Carolina - A second sampling station (Hewletts
Comparison of Biological Creek) was chosen as a test site for the
assessment of nonpoint impacts.
Metrics Derived From Hewletts Creek receives runoff from
Ponar, Epibenthic Trawl, central Wilmington. It has occasionally
and Sweep Net Samples: received pump station overflows, and its
A North Carolina Pilot shoreline is heavily developed with
Study single family residences. The large
quantities of macroalgae (Enteromorpha,
13.4.1 Study Objectives Ectocarpus, and Porphyra) that have been
flushed out of the creek could indicate
A test was designed to compare potential excess nutrients. The Hewletts
biological metrics derived from three Creek station was characterized by hard-
sampling methods, to determine which packed medium sand and shell
methods and metrics best demonstrated substrates, intertidal oyster bars and
differences between sampling sites saltmarsh.
(Eaton 1994).
A sampling station located in Bradley
Test data consisted of benthic Creek was selected as a representative
assemblage collection results for petite impaired area. Most of this watershed
ponar, epibenthic trawl and sweep net has been heavily developed, and the
samples taken in the vicinity of lower portion of the creek supports two
Wilmington, North Carolina (Figure 13- marinas. Sampling was conducted just
1). The data set included February and upstream from one large marina and
May 1993 ponar samples, November immediately downstream from the U.S.
1993 trawl and sweep net samples, and Route 76 bridge. The Bradley Creek
February 1994 samples using each of the station was characterized by mud and
three collection methods. muddy sand substrate, intertidal oyster
bars, and seasonally common
13.4.2 Study Location macroalgae (Ectocarpus).
Three sampling sites were located in 13.4.3 Study Methods

polyhaline (>20-ppt) waters in the
Wilmington vicinity. Howe Creek, a Three types of gear were employed to
primary nursery area north of sample the benthic assemblages at each
Wilmington, was selected as a reference station. A petite ponar was used to
site. Development in the Howe Creek collect three replicates of 1-3 grabs each
area was sparse residential on the north (depending on faunal density), thereby
side of the creek with a new sampling the infauna in a 0.04-0.13-m2
development on the south side. Samples area at each station. An epibenthic trawl
were collected on the north side of the (1.25-m net mouth) was pulled over 4-m
creek, which placed a large saltmarsh of unvegetated substrate to collect the
between the collection site and the epifauna and obligate infauna in a 5-m2
development to reduce possible impacts. area at each station. This method is
The Howe Creek sampling location was further described in Section 9.5. A D-
characterized by sand and shell frame net was swept through all
substrata, abundant sponge and oyster available habitats for 10-minutes,
populations, and seasonally abundant collecting the epifauna and shallow
macroalgae (Ectocarpus and Cladophora). infauna in a 20- to 60-m2 area.
Advantages and disadvantages noted
for each collection method are listed in identified to the lowest practical
Table 13-10. taxonomic level (usually species).
All samples were preserved in the field Biological metrics taken from a wide
with 10% formalin with Rose Bengal dye variety of sources were tested for each
added as a tissue stain. Samples were sampling method. It was expected that
returned to the laboratory, where they different metrics would prove useful for
were sorted from the detritus, then different sampling methods. Test
Table 13-10. Advantages and disadvantages noted for the three benthic assemblage collection
methods.
METHOD ADVANTAGES DISADVANTAGES
Petite Ponar • can be used in any depth water • it sam ples a rela tively sm all
on almost all substrates (except area, therefore rare and/or
hard bottom s). large taxa may not be
• most previous researchers used collected.
dredges, therefore some • the infauna are the most
com parisons with historic data tolerant portion of the
can be m ade . benth ic com m unity,
• true replication allows for therefore minor stresses
statistical treatment of the data. may be easily missed.
• sorting through large
amounts of sediment and
counting hundreds of
individuals of one or two
taxa can become tedious.
Ep ibenth ic • epifauna are ge nerally m ore • results are not co m parable

Trawl intolerant to stresses than with m ost historic
infauna, the refore m ore subtle databases.
environmental changes can be • the trawl is fairly unwieldy
detected than with infaunal and takes training to use
sampling. properly.
• a larger area is sampled than • it is im practica l to use in
with dredges, therefore m ore depth s beyond 5-1 0 m or in
rare taxa should be collected. strong currents (>1.5-2
• whe n op erate d pro perly, a m /s).
relatively small amount of
sedim ent is collected, therefore
sorting is not tedious.
Timed Sweep • a large num ber of taxa are • m etho d is lim ited to
collected including rare, large wadeable areas.
and intolerant taxa. • large amounts of sediment
• since m etrics are m ore re liable are usually collected,
when calculated with increasing mak ing sorting tedious.
observations (taxa), change in a • a higher degree of
metric is a more reliable indicator tax onom ic expertise is
of environmental change. required than needed for
• being semi-quantitative, only an the other methods.
estim ate of a bundance is • results are not co m parable
requ ired rather than h aving to with m ost historic
count each individual. databases.
• all habitats are sampled,
therefore loss or degradation of
habita t is m ore re adily
documented.
13-26 Case Studies

metrics included: Farrell Biotic Index unknown water quality. Lines in the
(modified for North Carolina), number figure represent possible break points
of amphipods and caridian shrimp, total for future criteria.
taxa, percent annelid abundance,
percent mollusc abundance, Shannon- Two metrics, Biotic Index (BI) and %
Wiener diversity index, amphipod Oligochaete and Pelecypod abundance
abundance, polychaete abundance, (% O&P), correctly ranked the three sites
molluscan abundance, gastropod sampled using an epibenthic trawl
abundance, bivalve abundance, (Table 13-11). In February, but not in
capitellid polychaete abundance, May, the %O&P was low because two
spionid polychaete abundance, taxa made up 70% of the individuals at
Hurlbert's PIE, Keefe's TU, Simpson's D, this site. This heavy skewness in
and oligochaete and pelecypod abundance may be due to seasonal
abundance (Engle et al. 1994; Farrell, recruitment. To date, these samples are
1993b, Nelson 1990, Washington 1984, the only collections made using the
Weisberg et al. 1993). All metrics were modified trawl. More samples are
tested using the data generated from required to adequately test the efficacy
each of the three collecting methods. A of the trawl.
metric was deemed to work if it was
able to correctly rank the stations; i.e., as The sweep method had three metrics
reference, slightly impaired, or heavily that ranked the three sites correctly
impaired. Those metrics that correctly (Table 13-11): Biotic Index (BI), Total
ranked the stations were further tested Taxa (TT), and Amphipod and Caridean
on a larger database to determine if Shrimp Taxa (A&C). Graphs of BI, TT,
metric ranking was a spurious and A&C values for 63 timed sweep
coincidence or was due to the samples over a range of salinities are
measurement of a consistent component presented in Figure 13-4. Each metric
of the biological community. appeared, in varying degrees, to be
affected by salinity. At sites where
13.4.4 Results salinities were above 8-ppt, there was
sufficient separation between Reference
Metrics that correctly ranked the three sites (diamonds) and Impacted
sites and their values, are listed in Table (triangles) sites to identify sites with
13-11 by sampling method. The Biotic Intermediate impact (squares) as well.
Index was the only metric to correctly This separation was smaller in
rank the sites; i.e., as reference, slightly intermediate salinities (8-20-ppt) than
impaired, or impaired for each of the higher salinities (>20-ppt). Samples
three collection methods. For samples collected below 8-ppt salinity showed a
collected by petite ponar, the Biotic limited range of metric values. Only BI
Index correctly ranked the sites for the was able to separate Reference from
two February samples, but failed to Impacted sites in these low salinities.
correctly rank the sites in May. This
may be related to seasonal fluctuations The Total Taxa metric may be related to
in recruitment (Holland 1985). The the habitat diversity of an area; a
Biotic Index as a function of salinity at diversity of habitats at a site would
38 sites sampled via petite ponar is include more niches, thus allowing the
presented in Figure 13-3. Diamonds survival of more taxa. This suggests that
represent reference sites, triangles the Total Taxa metric could serve as a
represent impacted sites and squares habitat quality measure as well as a
represent areas of intermediate or measure of water quality.
Table 13-11. Functional metrics for the three benthic assemblage collection methods.
Howe Creek Hewletts Creek Bradley Creek (Urban

(Reference Station) (Nonpoint Source Impact Station)
Impact Station)
Petite Ponar
Date 2/93 5/93 2/94 5/94 2/93 5/93 2/94 5/94 2/93 5/93 5/94 5/94
Biotic Index 2.7 2.1 2.1 1.9 2.0 1.6 2.2 1.9 1.6 1.9 1.8 1.4
Epibenthic Trawl
Date — — 2/94 11/93 — 2/94 5/94 — 2/94 5/94 —

5/94
Biotic Index 2.8 — 2.4 2.7 — 1.7 2.0 —
— — 2.5 2.8
% Oligochaeta &
Pelecypoda 27 — 31 6 — 37 4 —
Abundance — — 21 3
Timed Sweep
Date — — 2/94 5/94 11/93 — 2/94 5/94 11/93 2/94 5/94 —
Biotic Index — — 2.4 2.5 2.2 — 2.2 2.0 1.8 1.8 1.9 —
Total taxa — — 109 95 94 — 91 105 45 60 68 —
Amphipoda &
Caridean shrimp — — 17 22 9 — 9 15 7 7 9 —
Figure 13-3
Ponar samples: Ponar Biotic Indices
biotic index vs.
salinity
3
2.5
Biotic Index
BI Reference
2
BI Unknown
1.5
BI Impacted
1
0.5
0 10 20 30 40
Salinity
13-28 Case Studies

Figure 13-4
Biotic Index
BI, total taxa and
amphipod and
4
caridean taxa by
3.5 salinity.
Biotic Index
BI Reference
3 BI Intermediate
2.5 BI Impacted
BI Unknown
2
1.5
0 10 20 30 40
Salinity
Sweep Total Taxa
180
160
140
120 T T Reference
Total Taxa
100 T T Intermediate
80 T T Impacted
60 T T Unknow n
40
20
0
0 10 20 30 40
Salinity
Amphipod & Caridean Shrimp Taxa
35
30
25 A&C Reference
A&C Taxa
20 A&C Intermediate
15 A&C Impacted
10 A&C Unknown
5
0
0 10 20 30 40
Salinity
Amphipods and caridean shrimp score. While this appears to
make up 10-15% of the total taxa at a adequately correct a previously
site. This correlation explains why the unaddressed problem in biocriteria
graphs of the TT and A&C metrics development, assessment of the
look similar. Since the Crustacea usefulness of this approach must
include many of the most intolerant await a validation study, which is
taxa in the estuary, the A&C metric beyond the scope of the exercise
may prove to be more sensitive to described here.
slight differences in water quality
than the other metrics tested. One 13.4.5 Summary
potential problem with the A&C
metric is that it, like TT, appears to be Test results indicated that there was
affected by habitat quality, especially no metric which consistently ranked
the presence or absence of seagrass the test stations in a priori order of
and shells. impact based on petite ponar
collections, though this may have
The next step, following method been due to confounding by a spring
selection and metric determination, peak in recruitment. The Biotic Index
was biocriteria development. In this ranked sites correctly most often.
exercise, sweep samples at sites above Epibenthic trawl results correctly
8-ppt were used because multiple ranked the test sites using the Biotic
metrics had been identified which Index and percent abundance of
showed a range of water qualities. Oligochaeta and Pelecypoda metrics.
For each metric, a value above the Further sampling with the epibenthic
Reference/Intermediate line (Figure trawl is required to determine
13-4) was scored five points whereas a whether it or the ponar will give more
value below the Intermediate/ reliable results in non-wadable areas.
Impacted line was scored 1. To The sweep method appeared to be the
increase sensitivity, the Intermediate most versatile of the three test
Impact area was subdivided: values methods, resulting in three metrics
in the upper 20% were scored 4 points, that correctly ranked the test sites. All
values in the middle 60% were scored metrics appeared to lose sensitivity at
3 points, and values in the lower 20% salinities below 20-ppt. Possible
were scored 2 points. Points for each seasonal effects and differences in
of the three metrics were summed, substrate appeared to be confounding
giving each site a total score between the analyses as well; therefore, these
3 and 15 points. Water quality factors must be taken into account
bioclassifications were assigned based during the biocriteria development
on the number of points scored by a process. The Biotic Index appeared to
site (Figure 13-5). be the most versatile tool since it was
the only metric to correctly rank sites
An attempt was made, in step three of for all methods and all salinities.
biocriteria assignment, to address Initial efforts at biocriteria
natural situations where Taxa development in North Carolina will
Richness was depressed at a site (little focus on the Biotic Index as well as on
habitat diversity, wide salinity further sampling to determine the
swings, or high wave action). If one effects of seasonality, substrate,
or more of these situations could be salinity, and habitat variables.
identified for a site, an extra two
points were awarded to the total
13-30 Case Studies

Figure 13-5
Development of STEP 1: Assign points for each of three metrics from a sweep sample.
biocriteria.
Polyhaline (21 ppt to seawater)
Points 5 4 3 2 1
BI $ 2.6 2.59 - 2.5 2.49 - 2.01 2.0 - 1.91 # 1.9

Total Taxa $ 95 94 - 86 85 - 69 68 - 60 < 60
Amphipods & $ 21 20 - 18 17 - 13 12 - 10 9-0
Caridean Shrimp
Mesohaline (8 ppt to 20 ppt)
Points 5 4 3 2 1
BI $ 2.2 2.2 - 2.16 2.15 - 1.96 1.95 - 1.9 < 1.9

Total Taxa $ 38 37 - 32 31 - 24 23 - 18 17 - 0
Amphipods & $8 7 6-5 4 3-0
Caridean Shrimp
STEP 2: Sum points. This will yield a number between 3 and 15.
STEP 3: Check for Bonus Point conditions. Add 2 points to score if one or more
of the following conditions occurred: 1) Homogeneous habitat, 2) consistently high
wave action, 3) very high (>26 ppt/yr) salinity fluctuations.
STEP 4: Assign Bioclassification.
Bioclassification Points
No Impact 13-15
Slight Impact 11-12
Moderate Impact 8-10
Elevated Impact 6-7
Severe Impact 3-5
Primary Contact: Larry Eaton,

NC Division of Water Quality,
4401 Reedy Creek Road
Raleigh, NC 27602
919-733-6946
[email protected]
13-32 Case Studies
13.5 Indian River, Florida - limited the bottom salinity types
Field Verification of sampled to mesohaline, polyhaline, and
euhaline locations.
Marine Metrics Developed
For Benthic Habitats: The nature of pollution impacts in the
Indian River Lagoon, Indian River Lagoon presented a major
Florida Pilot Studies problem in sample selection. Maximum
impacts of pollution input (primarily
13.5.1 Study Objectives from urban runoff) are felt within the
small lagoonal tributaries as compared
A research program was developed for to the lagoon proper. Non-impaired
Florida estuaries to promote the tributary sites are generally not
identification of benthic marine available, which forces most reference
parameters indicative of relative water sites to be in the lagoon proper. This
resource quality (Nelson et al. 1993, sometimes resulted in a difference in
Nelson and Spoon 1994 a, b). The salinity between the impaired and non-
development of these parameters or impaired sites. For example, during
metrics was ultimately intended to help winter sampling, mean salinity at
quantify the diverse attributes and impaired sites was 13-ppt (mesohaline),
interrelationships of the community to: and was 25.3-ppt (euhaline) at non-
enhance documentation of possible impaired sites. However, these spatial
resource impairment from point and salinity differences appeared to be
non-point sources; evaluate aquatic life seasonal in the lagoon. Samples taken in
use attainment; and to be incorporated June had a mean bottom salinity of 25.3-
in the biological criteria process. ppt (euhaline) at impaired sites
compared to 29.6-ppt (euhaline) at non-
13.5.2 Study Methods impaired sites.
The process of developing benthic biota 13.5.3 Study Results

community parameters (or metrics)
indicative of Florida estuarine resource The benthic data were summarized in
quality was initiated in 1993 with Indian terms of: the mean percent of biomass
River Lagoon pilot studies (Figure 13-1). contained in the top five centimeters of
The initial study involved the collection the sediment profile at each of the
and analysis of samples taken from six stations; and the mean weight per
stations, including two within the main individual compared among sites and
Indian River Lagoon and four at the between the 0-5-cm and 5-15-cm depth
mouth of tributaries. Benthic samples segments. There was no clear difference
were collected by a diver using 8.2-cm in mean percent biomass (contained in
diameter Lexan cores which were the top 5-cm) between the two sets; i.e.,
sectioned into 0-5-cm and 5-15-cm depth impaired, non-impaired of sites. There
fractions. Study sites were selected with was also no clear difference in mean
the primary criterion of a presumed weight per individual based on
difference in pollution impact, with presumed differences in pollution
secondary emphasis on similarity of impact either for the surface sediments
sediment type and tertiary emphasis on or for the deeper sediments. Biomass
similarity in salinity. Three sites were differences with differing salinities also
designated impaired and three were showed no clear differences, in that
designated low impairment sites. The mean values of the percent total biomass
small scale or smaller number of stations above 5-cm ranged from 68% to 89% in
mesohaline areas, and 69% to 81% in < Spionidae/capitellidae ratio;
euhaline areas. The value in the single
polyhaline area was 94%. < Apparent color RPD depth.
Sediment types within the study area Of the seven metrics, separation
were classified as sand (>70% sand), between impaired and low impairment
mixed (30-70% sand), and mud (<30% sites was good for mean number of
sand). Both the impaired and non- species, percentage of amphipods,
impaired sites had all sediment types percentage of spionids, spionidae/
represented. There were no apparent capitellidae ratio, and apparent color
trends in biomass data among the RPD depth. The percentage amphipod,
sediment types. There was no percentage spionid, and
indication that sand sites had less spionidae/capitellidae ratio metrics
biomass in surface sediments than require separation of individual
mixed sediments, or that mean weight specimens which requires greater time
per individual differed among sediment than simple counts of total individuals
types. or total biomass. However, these
metrics seemed to offer much greater
During the initial studies, benthic data powers of resolution than measures of
were also summarized in terms of total total individuals or biomass.
individual and total species metrics.
The mean percentage of total Limitations on the generality of the
individuals present above 5-cm ranged conclusions of the initial pilot study
from 96 to 99.6% at the study sites. The were imposed by the limited number of
differences in this metric between sites sampling sites (6) and by the fact that
of different pollution impact was thus samples were obtained at only one point
very low; therefore, this metric did not in time. Seasonal variation in benthic
clearly distinguish Indian River Lagoon systems can be substantial; therefore, it
sites. Mean percentage of species above was essential to verify the temporal
5-cm in the sediments was calculated generality of initial conclusions.
from the data by dividing the total Similarly, spatial variations in salinity
number of species in the 0-5-cm fraction regime have been demonstrated to
by the sum of this value plus the total influence metric values. Therefore,
number of species recorded in the more extensive spatial and temporal
5 -15-cm fraction for each site. There sampling was warranted to verify the
was no clear separation between the utility of the proposed metrics. To
sites based on this metric. provide temporal verification of metrics,
the six sites originally sampled in
The initial Indian River Lagoon pilot January 1993 were resampled, and two
study and previous studies of the area new sites were added to the sampling
have examined the following metrics: plan to represent additional spatial
coverage of the Indian River Lagoon.
< Mean total number of individuals; The two additional sites were located
near Cocoa, Florida, with one presumed
< Mean total number of species; to be an impaired; i.e., located near a
sewage outfall pipe, and the other a low
< Percentage of amphipods; impairment site. Core samples were
collected by divers (as in the initial pilot
< Percentage of spionids; study) during June, July and August
1993. All organisms collected were
13-34 Case Studies

subsequently identified to the lowest i.e., percent of total, failed to clearly
feasible taxon, counted, oven dried, and distinguish the two types of sites.
weighed in the laboratory. Surface Comparisons of amphipod total
water temperatures and salinity, and abundance; i.e., amphipod total count,
bottom salinity measurements were also failed to clearly distinguish
made in the field, and sediment samples impaired versus low impact sites,
were collected by skin diving. One of ranging from 4-1789 at low impact sites
the proposed metrics was to involve and 27-62 at impaired sites. The 1993
visual determination of the apparent summer results contrast strongly with
color RPD depth. It was difficult to the winter results for the amphipod
measure a visual RPD with any degree metrics. Winter data showed clear
of confidence since the surface layers of separation of impact versus low impact
sediment were often flocculent and were stations with respect to both percent
therefore disturbed by the coring abundance and total number of
process. Attempts to measure the amphipods, whereas summer data did
apparent visual RPD were therefore not.
abandoned during the second phase of
pilot studies. The ratio of spionid polychaete
abundance to capitellid polychaete
A total of 64 benthic cores and 128 core abundance showed only partial
fractions were collected and processed separation between station types in the
during the second phase of pilot studies. summer samples. There was a
There was no clear distinction for the 0- decreased degree of separation with this
5-cm sediment fraction in mean number metric in summer versus winter
of individuals per core recorded at low samples. The differences in the ratio
impaired versus impaired stations. were generated both by reduced
Mean number of benthic taxa recorded numbers of spionids and by increased
per core from the 0-5-cm fraction also numbers of capitellid polychaetes at the
failed to show clear differences between low impact sites for winter samples. In
the two sets of stations. Clear contrast, differences in summer samples
distinctions were observed, however, for the low impact sites were mainly
between the impaired and low impaired caused by high values for capitellids.
sites with respect to mean abundance Therefore, a total capitellid metric was
per core for benthic organisms in the 5- examined for both seasons. Clear
15-cm fractions. Abundances in the 5- separation between impaired and low
15-cm fractions differed by a factor of at impact sites was given for this metric for
least 4 between the two sets of stations; both summer and winter data.
i.e., mean equaled 0-1.3 at impact Examination of a total annelid
stations and 5-10 at low impact stations. abundance metric also demonstrated
Impaired and low impaired sites also separation of impaired and low impact
showed clear separation based on the sites (for summer data).
mean number of taxa per core in the 5 -
15-cm fraction. Total faunal biomass showed no
separation of stations for either the 0-5-
The total species richness of amphipod cm or 5-15-cm core fractions. Expression
crustaceans was seven at both the of the biomass values above 5-cm were
impaired and low impact sites, and the modified by subtracting biomass for the
species recorded were similar. The occurrence of a few large organisms
metric based on the percentage (e.g., large bivalves). The adjusted
abundance of amphipod crustaceans; surface biomass metric also failed to
clearly separate the impaired and low The pilot study results clearly indicate
impact sites. that the season during which sampling
takes place may influence the ability of a
Differences in the values of benthic given metric to distinguish among sites.
community parameters were apparent Overall, clearer separation was seen
in summer samples as compared to the among sets of stations for winter
winter samples from the same study sampling than for summer sampling.
sites. The seasonal changes in This appeared to be related to the fact
abundance were anticipated given that highest organism density in Indian
previous knowledge of seasonal River Lagoon benthos is seen during late
abundance patterns of macrobenthos in winter, rather than in the summer as is
the Indian River Lagoon. Some the case at other locales. This clearly
proposed metrics were consistent in points out the need to evaluate
their performance in both winter and seasonality at specific geographic areas.
summer samples (Table 13-12). Both
abundance and taxa richness in the deep Relatively few of the proposed metrics
sediment fraction were metrics which consistently separated sites in the Indian
gave clear separation in the sets of River Lagoon. The mean abundance of
stations in both winter and summer. organisms and mean species richness in
Abundance of capitellids also the 5-15-cm depth fraction, and
consistently separated the station types capitellid abundance metrics all
during both seasons. provided consistent separation of station
types. The relatively small sample size
The performance of some of the metrics in terms of number of stations appeared
which appeared promising in the winter to result in ambiguous interpretation;
samples was somewhat altered in i.e., clear station separation ability in
summer. For example, taxa richness in winter and marginal in summer, for the
the 0-5-cm fraction, percent amphipod total amphipod abundance and
abundance, total amphipod abundance, spionid/capitellid ratio metrics. The
and spionid/capitellid ratio metrics natural temporal variability in the
discriminant stations in the winter, but benthos may be sufficiently extreme to
did not do so (or gave unclear results) in affect the performance of these metrics;
the summer. Explanations for this therefore, the best way to minimize the
change in performance may be complex. influence of the variation may be to
sample as many stations as possible.
The biomass measurements used in the
pilot studies were made on specimens In the most recent phase of pilot studies,
separated into lowest identified two amphipod metrics - mean number
taxonomic units, which required of amphipods per site and the ratio of
considerable time and effort. Had the Corophiidae/(Ampeliscidae +
biomass measures provided clear Phoxocephalidae) - were assessed at a
separation of station types, it would total of ten stations within the Indian
have been warranted to suggest that all River Lagoon. The original eight pilot
specimens be pooled to obtain a single sites were resampled and two additional
biomass value. However, it did not sites were sampled during May and
appear that biomass values for either June 1994, using techniques as described
depth fraction were useful as a benthic for the earlier pilot studies. A total of 80
metric for the Indian River Lagoon. benthic cores were collected and
processed.
13-36 Case Studies

Table 13-12. Comparison between winter and summer samples of the ability of the various metrics
tested to discriminate between impaired and low impairment sites.
M ET RIC WINTER SUM MER
0-5 cm abundance NO NO
5-15 cm abundance YES YES
0-5 cm taxa richness YES NO
5-15 cm taxa richness YES YES
percentage amphipods YES NO
total amphipod abundance YES ?
spionid/c apitellid ratio YES ?
capitellid abundance YES YES
total annelid abundance NO YES
total biomass NO NO
total biomass (excluding large ?

bivalves)
m ean perc ent biom ass abo ve NO NO

5 cm
NOTE: ? indicates marginal utility of metric due to inconsistent discrimination of impaired
and low impairment sites.
Results of collection analyses showed Primary Contact: Dr. Walter G. Nelson,

that the simplest amphipod metric, National Health & Environmental
mean total abundance, clearly separated Effects, Research Laboratory/ORD
impaired from low impact sites in the Western Ecology Division,
late winter samples taken in 1993. Hatfield Marine Science Center
However, summer 1993 and 1994 results 2111 SE Marine Science Dr.
indicated that the response of this metric Newport, OR 97365-5260
was not satisfactory. Available water 541-867-4041
quality information suggests a division [email protected]
of the set of 10 stations into three
groups: high impact, moderate impact,
and low impact. Use of the mean
number of amphipod metric did not
provide a similar separation of sites for
summer 1994 sampling data. However,
the outcome of the Corophiidae/
Ampeliscidae metric calculations was
most consistent with the high impact,
moderate impact, low impact division of
sites, and therefore appeared to
reasonably reflect water quality
conditions of the Indian River Lagoon.
13-38 Case Studies
13.6 Ocean City, MD — the Ocean City outfall (Figure 13-7).
This structure provides a set of control
Bethany Beach, DE — A
or reference stations for comparison to
Preliminary Study of the the test stations at “C” and “G”. Each
Use of Marine Biocriteria station is located with differential GPS
Survey Techniques to with an estimated precision for the
Evaluate the Effects of receiver of +/- 5-m.
Ocean Sewage Outfalls in
the Mid-Atlantic Bight The variables measured are benthic fish
and macroinvertebrate communities as
13.6.1 Study Objectives reflected in indexes and metrics
incorporating number of taxa and
This project investigates the practical, number of individuals per taxa. Fish
low cost application of marine biological surveys are made with a 6-m (5-m
community measurements and the near effective opening), 2.5-cm mesh otter
field/far field survey technique for use trawl. Tows are made parallel to the
by coastal States as a water resource shoreline at 1-ms-1 over 0.9-km with the
quality management tool. The methods station coordinates located at the mid-
applied here are derived from work point of the tow. Trawl scope used is six
reported by Pearson and Rosenberg to one. Benthic macroinvertebrate
(1978) and Mearns and Word (1982) samples are collected with a 0.1-m2
with modifications. Smith-McIntyre grab or with a 0.1-m2
Young grab, and three replicates are
13.6.2 Study Methods taken for each sample at each station site
as indicated by DGPS coordinates.
The study area is a 16-km coastal reach Ferraro et al. (1994) reviewed their
between Bethany Beach, Delaware and extensive data base and concluded that
Ocean City, Maryland (Figure 13-1, 13- five replicates with a 0.02-m2 petite
6). These are nearly adjacent resort ponar grab, each sub-sampled with four
communities on the Mid-Atlantic 8-cm diameter cores is optimal for
seaboard between Delaware Bay and waters of the Southern California Bight.
Chesapeake Bay. Each has a secondary We elected to use the 0.1-m2 grab with
treatment municipal sewage discharge three replicates, but to count the entire
site about 2.8-km offshore. Discharge is grab. This was judged to be a
in both cases through a diffuser at a reasonable compromise between more
water depth of approximately 12-m. replicates and the uncertainty of sub-
The Bethany Beach sewage treatment sampling a site for which there was
plant average discharges about inadequate preliminary information.
0.61-m3 s-1( 14-mgd) and Ocean City From this data base we hope to make
about 1.4-m3 s-1 (32-mgd). further sampling refinements in the
future. Identifications of collected
A series of nine north-south trending organisms are to species whenever
stations were installed parallel to the possible. All survey work was
coast at intervals of about 2-km, each in conducted from the USEPA Ocean
about 12-m depth of water and over Survey Vessel Peter W. Anderson. The
medium to fine sandy bottoms to obtain Anderson is a 50-m research ship, but all
a similarity of habitat as much as equipment used and methods employed
possible. The stations are labeled “A” are appropriate for deployment from a
through “I”, with station “C” at the 15-m vessel typically used by most
Bethany Beach outfall and station “G” at coastal States. Incidental to this project,
Figure 13-6
Bethany
Beach - Ocean
City study
area.
a comparison of the Smith-McIntyre and Sampling surveys have been conducted

Young grabs was made. Six replicate twice a year in July-September and
drops with each grab were made at January-February since 1993 to
three sites characterized by: hard determine if multiple season indexing is
packed fine sand; medium grain sand; necessary or appropriate. While the
and coarse sand and gravel. Either gear Mid-Atlantic area is considered to have
was judged acceptable, but the Young four discrete seasons, benthic
grab was less inclined to wash. communities are expected to be in flux
13-40 Case Studies

Figure 13-7
Bethany
Beach - Ocean
City sampling
locations.
during Spring and Fall and to be most sieved on board using a 0.5-mm mesh
stable in Summer and Winter screen after recording a physical
(Ranasinghe et al. 1994). description of the sample and taking a
2.5-cm diameter subcore for grain size
Fish sample processing is conducted on analysis. The retained material is fixed
board with all individuals identified to in 10% buffered formaldehyde with
genus and usually to species. Length Rose Bengal dye added. Taxonomic
measurements (TL) are made and any identifications and counts are made later
gross anomalies recorded. The fish are at laboratory facilities ashore with most
returned to the water as soon as identifications carried to the species
measurements are completed. Benthic level.
invertebrate sediment samples are
To make comparisons between the and recorded throughout the
sample sites, habitat control in the water column.
survey design was maintained as well as
possible by attention to three major To date, these variables have been
variables: consistent over the length of the transect
for each cruise.
1) Grain size of bottom sediments.
This also reflected a habitat In keeping with the objective of low
impact of the discharges when cost, practical applications of biological
fine sediments were deposited in community measurements for resource
bottom depressions near the impact detection; standard, basic but
outfalls. At the beginning of the robust taxonomic indexes were applied
project, sediment samples were to the data. The underlying premise for
collected from all nine stations the indexes is that once the raw data for
and analyzed for heavy metals species and numbers of individuals per
and a for a standard array of species are compiled, the investigator’s
toxicants. All results were primary question is whether or not there
insignificant, suggesting no other is a detectible impact. More refined
sources of biotoxicity or indexes and indicators can later be
impairment indigenous to the applied or developed as needed. In this
immediate area. regard, the treatments selected for this
project were: total number of
2) Water depth. Water depth over individuals, total number of taxa
stations “A” through “E” ranges (species), evenness index, Simpson’s
from 11-m to 14-m with the dominance index, Margalef’s taxa
variation accounted for by a richness index, and Shannon-Wiener
general ridge and swale index of general diversity. The
bathymetry off Bethany Beach. appropriate equations were taken from
From “E” through “I”, the Odum (1971).
variation is from 14- to 16-m,
accounted for by an east-west 13.6.3 Study Results
ledge with about a 3-m drop just
south of the Ocean City outfall. Fish Survey Data
Subsequent data analyses
suggest that these variations in Analysis of the fish data showed no
water depth do not restrict fish significant differences in trawl data
or invertebrate distributions over between the stations in either summer or
the area. winter collections for either number of
taxa or numbers of individuals. These
3) Water quality. At the outset of results are based on single tows at each
the study, and each time station twice a year (summer and
biosurveys are conducted, winter) for three years. Concern that
multiple depth and standard this response results from too little data
water quality measurements are led to a trial in summer 1995, with three
made using a Sea-Bird SBE-9 replicate trawl surveys over the nine
“CTD” probe. Conductivity, stations, i.e., sequential tows of stations
temperature, depth, dissolved “A” through “I” conducted three times
oxygen, pH, transmissivity, and in one day. The results were still
chlorinity/salinity are measured insignificant. Better results might be
possible by replicating each station
13-42 Case Studies

individually. Eaton (1994) reported that variables that characterize community
for West Coast fish surveys in a structure.
Washington estuary, four replicate tows
per station are necessary to obtain However, in this instance, it appears
meaningful data within a fairly confined that at least some indexes enhance the
waterway. Qualitatively, taxa and measurement of outfall perturbations.
number of individuals overall shifted Box plots of Simpson’s dominance index
considerably between summer and (Figure 13-10a, b), the Shannon-Wiener
winter surveys at the nine stations. index of general diversity (Figure 13-
Greater numbers of both species and 11a, b), and particularly Margalef’s
individuals (excepting winter runs of richness index (Figure 13-12a, b) (Odum
striped anchovy, Anchoa hepsetus) occur 1971), over the three years of summer
in the summer surveys. data provide strong indications of the
negative effect of both discharges on the
Benthic Macroinvertebrate Data benthic macroinvertebrate community.
Benthic macroinvertebrate results have 13.6.4 Discussion and Conclusions

been much more promising, but the
same seasonal trend observed for fish The nearfield/farfield survey design for
for number of taxa and number of biological surveys, together with basic
individuals has prevailed. Summer indexes of community structure, appears
measurements are much more indicative to work equally well on the West coast
of the condition of the benthic and in Mid-Atlantic coast open water
macroinvertebrate assemblages (some of environments (Santangelo, pers. comm.
the winter data is incomplete). The data 1996). If the investigator is careful to
in this instance is for three replicates at control for habitat characteristics, the
each station twice a year for three years. ends of the transect can serve as a
Significant differences are evident reference condition, the outfall stations
between each of the outfall sites and the as test sites, and the intermediate
other stations in the summer data stations provide an indication of the
(Figure 13-8a,b). The graphic data for gradation of impact(s). The nine station
number of individuals is intriguing in design of this study made it possible to
that it suggests enhanced and or treat the data as a combination of two
enriched conditions at station “A”, impact sites on the ambient
perhaps from the Delaware Bay environment, or as two individual
discharge, and at the Ocean City outfall studies in tandem.
site.
Summer benthic macroinvertebrate data
When numbers of species are compared, from stations “A” and “C” were
a more negative trend in outfall impact significantly different in either case,
is evident, especially for the Bethany lending confidence to the conclusion
Beach outfall station (Figure 13-9a). A that the wastewater discharges were
similar pattern occurs at Ocean City, but having a measurable impact on the
is not as strong (Figure 13-9b). Ludwig coastal marine environment. This is of
and Reynolds (1988) state that a simple particular interest because routine water
count of the number of species present, quality and sediment investigations at
for samples of equal size, avoids some of the sites failed to consistently detect
the problems of using indexes which change between the outfalls and the
combine and may confound a number of surrounding stations. The biocriteria
technique employed appears to be not
10000
Figure 13-8a
Total number
of macro-
Total Number of Individuals
invertebrate
individuals at
1000 Bethany
Beach sites;
summer
data, n=9.
100
Max
Min
75%
25%
10
A B C D E Median
Station
Figure 13-8b
10000
Total number
of macro-
Total Number of Individuals
invertebrate
individuals at
Ocean City
1000 sites;
summer
data, n=9.
100
Max
Min
75%
25%
10
F G H I J Median
Station
13-44 Case Studies

Figure 13-9a
90
Total number
of macro-
80
invertebrate
taxa at
Bethany 70
Total Number of Taxa

Beach sites;
summer 60
data, n=9.
50
40
30
20
Max
Min
10
75%
25%
0
A B C D E Median
Station
Figure 13-9b
90
Total number of
macro-
invertebrate taxa 80
at Ocean City
sites; summer 70
data, n=9.
60
50
40
30
20
Max
Min
10
75%
25%
0
E F G H I Median
Station
Figure 13-10a
90
Simpson’s
dominance index
80
for macroinverte-
brates at Bethany
70 Beach sites;

summer data,
60 n=9.
50
40
30
20
Max
Min
10
75%
25%
0
A B C D E Median
Station
Figure 13-10b
90
Simpson’s
dominance index
80 for macroinverte-
brates at Ocean
70 City sites;
summer data,
60 n=9.
50
40
30
20
Max
Min
10
75%
25%
0
E F G H I Median
Station
13-46 Case Studies

Figure 13-11a
3.5
Shannon-Wiener
diversity index for
macro-
Shannon-Wiener Index Value

3.0
invertebrates at
Bethany Beach
sites; summer
data, n=9. 2.5
2.0
1.5
1.0 Max
Min
75%
25%
0.5
A B C D E Median
Station
Figure 13-11b
3.5
Shannon-Wiener
diversity index for
macro-
Shannon-Wiener Index Value
invertebrates at 3.0
Ocean City sites;
summer data,
n=9. 2.5
2.0
1.5
1.0 Max
Min
75%
25%
0.5
E F G H I Median
Station
Figure 13-12a
Richness index
for macro-
10 invertebrates at
Bethany Beach
sites; summer
Richness Index Value
data, n=9.
8
4
Max
Min
75%
25%
2
A B C D E Median
Station
Figure 13-12b
Richness index
for macro-
10 invertebrates at
Ocean City sites;
summer data,
Richness Index Value
n=9.
8
4
Max
Min
75%
25%
2
E F G H I Median
Station
13-48 Case Studies

only practical, but sensitive as well, coastal and estuarine biosurveys.
detecting impacts that might not However, the fish community does
always be observed with routine not appear to be very responsive to
chemical testing. Standard indexes sewage discharge effects in this
such as Margalef’s Richness Index, coastal area. This is probably because
Simpson’s Dominance Index and of the mobility of the fish in these
Shannon-Wiener’s Diversity Index are open coastal waters, their seasonal
robust and were entirely appropriate migrations, and the potential sport
for this survey. and commercial fishing pressure
confounding the survey effort; but the
The Smith-McIntyre and Young grabs sampling replication factor was not
were both entirely adequate, but the adequately investigated in this study.
Young was more efficient and safer to
work with, while the Smith-McIntyre For biocriteria development and site
was more accessible through the top monitoring, it is important to account
for sub-sampling. Three replicate for seasonality. For the Mid-Atlantic
grabs were sufficient to generate Bight, late June to early September
meaningful data, but it may be appears to be a time of relatively high,
possible to reduce the costs of the stable community productivity and an
taxonomic operation by sub-sampling optimal index period if once a year
the grabs. An attempt was made to do sampling is preferred. According to
this by mechanically splitting the the Delaware and Maryland chambers
intact samples in half with a sheet of commerce, since Bethany Beach and
metal partition. It failed because the Ocean City are summer resort
surficial organisms were unequally communities, their populations
distributed as the sample drained and increase at least ten-fold in warm
the ship rolled. Subcores of 5-cm weather (pers. comm. 1990). Their
diameter might be a better alternative lower winter discharge rates, together
requiring far less analytical effort. with a natural cyclic depletion of the
Similarly, sieving and counting only marine community, may account for
the top 5-cm of the sample as a the failure of our data to reveal
variation of the technique reported by sewage impacts in this season. This
Diaz in Gibson et al. (1993) might be a may not be the case with a year-round
more cost-effective approach. municipality of fairly large size. In
Another alternative to reduce the any case, if the responsible agency can
number of organisms dealt with is to afford to sample at least occasionally
double the sieve size to 1.0-mm, as in winter, that baseline biological data
practiced by many investigators. Any may prove invaluable in the event of
of these options could be explored and oil spills or other marine accidents.
adopted as a cost-effective way to
accomplish the benthic macroinverte- After the assessment of results from
brate counts as long as the an initial set of 1.6-km interval station
investigator ascertains that they transects, the investigator may choose
produce reliable results consistent to delete some of the intermediate
with those derived from the larger reference stations and replace them
grab samples. with a more diagnostic set of near
discharge monitoring stations. It will
The 6-m otter trawl used in the fish then be possible to assess the relative
surveys performed well and is expansion or contraction of the area of
believed to be appropriate for both impact over time and in response to
plant operation declines or to this control to assess the relative
improvements. The initial and efficacy of this technique as a cost
subsequent reference site data become saving approach for these waters. The
part of the biocriteria which can be process was repeated during the
used as a benchmark to assess summer of 1997 and the results of
operational efficiencies, management both trials will be evaluated when
initiatives, and the adequacy of taxonomic studies, which were
NPDES permits. delayed (for this and the above study)
are completed.
Additional investigations for which
results are pending 3. Because of the promising results of
this project so far, three additional
1. Because vertical splitting of each stations have been added around each
grab sample was determined to be an outfall station, e.g., “C” at Bethany
unsatisfactory approach to reducing Beach and “G” at Ocean City. The
sample volume and cost, we are pattern creates a roughly equilateral
attempting to test a horizontal triangle with approximately 0.46-km
approach at approximately the 5-cm legs and a station at each apex with
depth level because most of the the original station in the middle of
organisms observed are the triangle. The intent here is to see if
predominantly surficial sediment it is possible to refine the spatial
dwellers. In September 1996, the assessment of the zone of impact for
stations were sampled with three each outfall analogous to the concept
replicate grabs as before, but illustrated in Figure 13-13.
approximately the top 5-cm of
sediment was scraped off of each 13.6.5 Use of the Bethany Beach-
sample and sieved through a 0.5-mm Ocean City Data to
mesh screen. The remainder of the Illustrate Biocriteria
sample was similarly processed. We Development
will count both fractions, combine the
results and evaluate as usual. An example of biocriteria
development using this pilot project is
This information will then be as follows.
compared to a similar assessment
using just the top 5-cm fraction. If the Classification and Reference Site
same impact information results, it Selection: A review of the data as
may be possible to monitor the presented in Figures 13-7 through 13-
stations using just the surface 12 suggests that stations A, E, and I
fractions as long as these results are are appropriate reference sites being
periodically calibrated against full at the center and extreme ends of the
grab counts. transect and equidistant from the
defined locales of effluent discharges
2. On the January, 1997 survey, all of being evaluated. General water
the stations sampled for benthic quality conditions, including salinity
macroinvertebrates were sieved first and depth, are consistent for all
through a 1.0-mm screen and then stations. Grain size, although shifting
through the 0.5-mm screen. These from sand and gravel in the north at
separate fractions can be combined to station A to sand at station I in the
produce a comprehensive result. The south represents the general benthic
1.0-mm fraction can then be compared habitat condition of the area with an
13-50 Case Studies

Figure 13-13
Proposed
diagnostic
net longshore current
nearfield station
array. A
B
C
D1 D3
discharge D D4
D2 D5
E
F
G
Data can be used to plot not only

impact, but relative expansion or
contraction of the area of impact over
time.
A B C E F G
D
SERIES
STATIONS
acceptable variation for the region. 13-13 presents the range of those
Thus, the stations (or sites) are values for the summer parameters
considered to all be of comparable measured at each of the three
habitat characteristics, and because of reference sites and the mean range of
the spatial arrangement, sites A, E, those scores. The range was selected
and I are selected as references. over mean or median values to
accommodate the variability of the
Reference Condition: The reference biological data. This mean range is
condition may be derived from the the reference condition or minimally
interquartile range of scores of the impacted (by human activities, e.g.
values of the biotic condition sewage discharge, all other factors
measured at the reference sites. Table being considered equal) condition for
Table 13-13. Establishment of reference condition using the mean of the interquartile range of scores for three
reference sites.
Inter-quartile Range of Values
Station Ind ividuals Taxa Sim pson ’s Shannon- Richness

Index Wiener
A 427-3049 46-71 0.075-0.161 2.597-3.137 7.3-9 .1
E 281-474 40-49 0.076-0.224 2.262-3.889 6.6-8 .0
I 136-841 27-42 0.129-0.260 1.993-2.524 5.3-6 .0
Mea n Score 281-1455 38-54 0.093-0.215 2.284-3.183 6.4-7 .7
important to note that the other

this Maryland-Delaware reach of the
elements of development of a
Mid-Atlantic Bight.
biocriterion should not be casually
dismissed. While the reference
Biocriteria: The elements of a
condition is essential, with a large
biocriterion are: (1) historical
available historical database these
information about the area; (2) present
present values might well be adjusted
reference condition information; (3)
either up or down to accommodate
empirical modeling of data if needed;
the historical trend for the area.
and (4) an assessment of this
preceding information by a locally
Assessment Comparing Biocriteria to
familiar panel of specialists.
the Test Sites: The test sites at “C”
(Bethany Beach, DE outfall) and at
(1) There is insufficient local historical
“G” (Ocean City, MD outfall) are then
information or data to establish a
compared to the biocriteria as
trend against which the reference
illustrated in Table 13-14.
condition data can be compared.
Neither outfall site completely meets
(2) The present reference condition
the range of criteria derived from the
data is presented above.
reference condition for any of the
metrics applied, although the Bethany
(3) The indexes used to compile the
Beach outfall approximates the
raw data constitute the only modeling
criterion for number of taxa present.
element since this is a site specific
It should be noted that the outlier at
assessment.
reference station “A” (perhaps caused
by Delaware Bay enrichment) raises
(4) The authors of this manual are
this criterion range at the expense of
surrogates for a panel of local
the Bethany Beach outfall. The Ocean
specialists which would likely consist
City outfall nearly fits the diversity
of USEPA, US Fish and Wildlife
index criterion. However the outfall
Service, NOAA, and State biologists
far exceeds the number of individuals
and water resource managers.
category by more than three times the
criterion. This reflects several
Consequently, the reference site data
instances when the benthic grab was
and index scores presented here
overwhelmed by polychaete worms, a
essentially comprise by default, the
condition usually indicative of sewage
candidate biocriteria for the purposes
pollution.
of this study. However, it is
13-52 Case Studies

Table 13-14. Comparison of the reference condition derived biocriteria to the interquartile range of scores at the
Bethany Beach and Ocean City outfalls.
Variable Bio criteria Bethany Beach Oce an C ity

Ou tfall Ou tfall
No. Indiv. 281-1455 260-1988 49-6,492
No. Taxa =/>38-54 28-43 13-49
Simps. Dom. =/<0.093-0.215 0.171-0.642 0.179-0.643
Shan.-Wien. DI =/>2.284-3.183 0.970-2.648 1.855-2.883
Richness =/>6.4-7.7 4.6-5 .8 3.1-5 .7
This instance of near exceedance of intensively monitored to determine if

one of the criteria in each case the zones of impact are expanding or
illustrates the importance of using contracting. The combined
several biological metrics to establish information of criteria comparisons
a reference condition which best and impact zone measurements
represents a diverse and healthy should provide valuable information
community, and which contributes to for NPDES permit evaluations at
more robust and sensitive biocriteria. Bethany Beach and Ocean City.
Conclusion: For a formal criteria This technique and evaluation

development program, more data are approach may prove particularly
required, but the indexes applied helpful as Eastern Seaboard
appear to ably translate the data into development continues to increase
workable criteria. Ironically, the and more coastal communities seek
number of individuals and number of ocean discharge permits for their
taxa metrics individually do not municipal effluents.
reflect apparent conditions as well as
the indexes which combine these Primary Contact: George Gibson, Jr.
primary variables. (4304), USEPA, Office of Water, Office
of Science and Technology
Recommendations: The stations 1200 Pennsylvania Avenue, NW
should continue to be monitored by Washington, DC 20460
USEPA Region III biologists and the 410-305-2618
data set further developed. The long [email protected]
term areal impact of the discharges
should be better assessed using the
additional near-discharge stations
described above. Changes in sieve
size and use of grab fractions, if
justified, will help reduce the cost of
the monitoring.
Eventually, as a further cost reduction

measure, it may be possible to
monitor just stations “A”, “C”, “E”,
“G”, and “I”. However, periodically
the outfall stations should be
13-54 Case Studies
13.7 Environmental Quality undegraded estuarine area were
compared to results of a related EMAP
of Estuaries of the survey conducted in 1994 in this same
Carolinian Province: region as part of a multi-year
1995 monitoring effort.
13.7.1 Background/Objectives 13.7.2 Methods
A study was conducted to assess the An overall goal of EMAP is to make

environmental condition of estuaries in statistically unbiased estimates of
the EMAP Carolinian Province (Cape ecological condition with known
Henry, VA - St. Lucie Inlet, FL; Figure confidence. To approach this goal, a
13-14). The objectives of this study are probabilistic sampling framework was
being addressed using a probability- established among the overall
based sampling design, under which a population of estuaries comprising the
large regionally extensive population of Carolinian Province. Under this design,
randomly selected sites is sampled from each sampling point is a statistically
year to year, following earlier EMAP-E valid probability-based sample. Thus,
designs (Strobel et al. 1994, Summers et percentages of estuarine area with
al. 1993). This design makes it possible values of selected indicators above or
to produce unbiased estimates of the below suggested environmental
percent area of degraded vs. guidelines can be estimated based on the
undegraded estuaries, based on a series conditions observed at individual
of indicators of environmental quality. sampling points. Statistical confidence
Overall, the objectives of the program intervals around these estimates also can
are to: be calculated. Moreover, these estimates
can be combined with those for other
< Assess the condition of estuarine regions that were sampled in a
resources of the Carolinian Province consistent manner to yield national
based on a variety of synoptically estimates of estuarine condition. This
measured indicators of section describes in brief how stations
environmental quality; were selected using the probabilistic
design (see also Rathbun 1994).
< Establish a baseline for evaluating Supplemental sites, selected non-
how the condition of these resources randomly in clean areas and in
are changing with time; suspected polluted areas, were included
in the survey and are discussed below.
< Develop and validate improved
methods for use in future coastal Sampling sites in 1995 consisted of 87
monitoring and assessment efforts. base stations and 21 supplemental
stations. Base stations were randomly
A total of 87 randomly located stations selected sites that made up the
were sampled from July 5 - September probability-based monitoring design.
14, 1995 in accordance with the Four replicate bottom grabs were
probabilistic sampling design. collected from each station with a 0.04-
Wherever possible, synoptic measures m2 young grab sampler. Data collected
were made of: 1) general physical
habitat condition, 2) pollution exposure,
3) biotic conditions, and 4) aesthetic
quality. Percentages of degraded vs.
Figure 13-14
1995 Carolinian
Province sampling
stations.
from these sites were used to produce mainly on the physical dimensions of an
unbiased estimates of estuarine estuary. Table 13-15 breaks down the
condition throughout the province estuarine resources of the Carolinian
based on the various synoptically Province by their size designation.
measured indicators of environmental Stratification of the overall sampling
quality. The province-wide distribution area into classes of estuaries with similar
of base sites is shown in Figure 13-14. attributes was necessary in order to
Supplemental stations were selected minimize within-class sampling
non-randomly in areas for which there variability. Also, it was not feasible to
was some prior knowledge of the sample all of the different types of
ambient environmental conditions. estuaries that exist within a broad
These sites, which represented both geographic region at the same spatial
pristine areas and places with histories scale. Stratification by physical
of anthropogenic disturbance, were used dimensions of an estuary was adopted
to test the discriminatory power of because: 1) such attributes usually show
various ecological indicators included in minimal change over extended periods;
the program. Data from supplemental 2) alternative classification variables
sites were not included in the such as salinity, sediment type, depth,
probabilistic spatial estimates. and extent of pollutant loadings would
result in the definition of classes for
As in other EMAP-E provinces (Strobel which areal extents could vary widely
et al. 1994, Summers et al. 1993), the from year to year; 3) data for physically
sampling design for the base sites in the based classes can be aggregated into
Carolinian Province was stratified based geographic units that are meaningful
13-56 Case Studies

Table 13-15. Estuarine resources of the Carolinian Province.
Province Large Sm all Large Tidal
Estuaries Estuaries Rivers
All Years
Num ber of 200 3 194 3
Estuaries
Area 11,6 22.1 5,58 1.1 4,907 1,134
Represented
(km 2)
In 1995
Num ber of 88 16 55 a 17 b
Stations
Area 6,99 1.8 4,48 0.0 1,37 7.8 1,134
Represented
(km 2)
a
Station count includes 6 replicate stations
b
Station count includes 3 replicate stations
from a regulatory or general-interest base stations to provide a consistent set

perspective; and 4) estuarine boundaries of synoptic data for making province-
can be delineated more readily and wide estimates of estuarine condition.
accurately from maps or charts of the These “core” environmental indicators
physical dimensions of coastal areas included measures of general habitat
than from maps of sediment or water- conditions, pollutant exposure, biotic
column characteristics. integrity, and aesthetic quality (Table 13-
16). Habitat indicators describe the
Selection of base-site sampling physical and chemical conditions of
approaches varied on the physical sample sites, and provide basic
characteristics of the particular estuary information about the overall
being sampled. Base sites in all estuaries environmental setting. Exposure
were selected using an approach similar indicators provide measures of the types
to the one used in the EMAP and amounts of pollutants, or other
Louisianian Province (Summers et al. adverse conditions, that could be
1993). In large estuaries, sites were harmful to resident biota or human
selected using a sampling grid health. Biotic condition indicators
approach. A triangular lattice was provide measures of the status of
placed initially over the study region biological resources in response to the
and the resulting grid shifted randomly. surrounding environmental conditions.
In large tidal rivers, base sites were Aesthetic indicators provide additional
selected randomly, using a “spine and measures of environmental quality from
rib” approach. Finally, base sites in a human perceptual perspective. There
small estuaries were selected using a is a fair amount of overlap among these
random list-frame approach, also similar various indicator categories. For
to the approach used in the EMAP example, some aesthetic indicators
Louisianian Province (Summers et al. (presence of oil sheens, noxious
1993). Table 13-16 lists the core sediment odors, and highly turbid
environmental indicators sampled at the waters) could also reflect adverse
various sites. exposure conditions. Another example
A standard series of environmental is dissolved oxygen (DO), listed as an
parameters was measured at each of the exposure indicator because of the
Table 13-16. Core environmental indicators for the Carolinian Province.
Habitat Indicators
W ater d epth
W ater temp erature
Salinity
Density stratification of water column
Dissolved oxygen concentrations
pH
Percent silt-clay conte nt of s edim ents
Percent TOC in sed iments
Se dim ent ac id-volatile sulfide s (Yr. 2 only *)
Expos ure Indicators
Low dissolved oxygen conditions
Sedim ent conta m inants
Contam inants in fis hes and inverteb rates (Yr. 2 only)
Sedim ent toxicity
Biotic Condition Indicators
Infaunal species composition
Infau nal sp ecies richnes s an d diversity
Infaunal abundance
Benthic Infaunal Index
Dem ersal species composition (invertebrates and fish)
De m ersal spe cies richness and divers ity
Dem ersal species abundance
Dem ersal species lengths
Externa l patho logica l abno rm alities in de m ersal biota
Aesthetic Indicators
W ater c larity
Anthropogenic debris (sea surface and in trawls)
Noxious sediment odors (sulfides, petroleum)
Oil sheens (sea surface and bottom sediments)
*
Resu lts not shown in this report
potential adverse biological effects of indicators, some still in the development

low oxygen concentrations, but which stage, are listed in Table 13-17. They
also is clearly a measure of general include sediment bioassays with
habitat conditions. These various core alternative test species, such as the
environmental parameters included amphipod Ampelisca verrilli as an
ones used in other EMAP-E provinces alternative to A. abdita in standard 10-
(Strobel et al. 1994, Summers et al. 1993) day solid-phase toxicity tests; assays
to support regional comparisons and to with additional sublethal biological
provide a means for producing endpoints, such as effects on feeding,
combined nationwide estimates of growth and fertilization success in key
estuarine condition. estuarine organisms; additional indices
of environmental quality for tidal
In addition to making the standard marshes and estuarine fish assemblages;
EMAP-E measurements, an emphasis and the incorporation of additional
was placed on developing and exposure indicators, such as porewater
validating other complementary ammonia and hydrogen sulfide
methods to aid in evaluating the quality concentrations, to help in the
of southeastern estuaries. Such
13-58 Case Studies

Table 13-17. Exposure indicators under development in the Carolinian Province.
10-d ay acute-to xicity sed iment bioassay with alternative am phipod s pec ies, Ampelisca
verrilli
1-we ek subletha l bioassay for tes ting effects o f sedim ent ex posure on gro wth of juvenile
clams Me rcenaria m ercenaria
96-hour sublethal bioassay for testing effects of sediment exposure on feeding rates of
Am pelisca verrilli
1-hour sublethal bioassay using gametes of oysters Crassostrea virginica and clams
Me rcenaria m ercenaria for testing effects of sediment exposure on fertilization success
Sediment porewater amm onia and hydrogen sulfide concentrations
interpretation of sediment toxicity data set representative of degraded and

results. undegraded sites in each habitat (3)
comparing various benthic attributes
13.7.3 Benthic Infaunal Index between reference sites and degraded
sites for each of the major habitat types;
The modified IBI approach of Weisberg (4) selecting the benthic attributes that
et al. (1997) was used to develop a best discriminated between reference
benthic index for southeastern estuaries. and degraded sites for inclusion in the
The goal was to develop an index that index; (5) establishing scoring criteria
possessed the following features: (1) (thresholds) for the selected attributes
suitable for use throughout the region, based on the distribution of values at
(2) applicable to a broad range of reference sites; (6) constructing a
habitats, (3) easy to understand and combined index value for any given
interpret, and (4) effective in sample by assigning an individual score
discriminating between undisturbed for each attribute, based on the scoring
and disturbed conditions associated criteria, and then averaging the
with human influences. individual scores; and (7) validating the
index with an independent data set.
Results of the 1994 survey (Hyland et al.
1996) indicated that several natural Data from undegraded sites sampled in
abiotic factors (salinity, latitude, silt- 1993 and 1994 were first analyzed using
clay, and TOC) had strong influences on classification (cluster) analysis of benthic
infaunal variables. In the IBI approach, species composition and evaluation of
an attempt is made to account for such the physical factors associated with the
variations by defining habitat-specific resulting station clusters to define major
reference conditions at sites free of habitat types. Several types of cluster
anthropogenic stress and then analyses were performed. The one that
comparing conditions in samples with produced the clearest results was a
the expected reference conditions for normal (Q-mode) analysis run on log10-
similar habitat types. The basic steps transformed data with flexible sorting as
used to develop the index involved: (1) the clustering method and Bray-Curtis
defining major habitat types based on similarity as a resemblance measure (see
classification analysis of benthic species Boesch 1977).
composition and evaluation of the
physical characteristics of the resulting
site groups; (2) selecting a development
Differences in abiotic factors (salinity, at " = 0.1). These six metrics were: mean
latitude, % silt-clay, TOC) among the number of taxa, mean abundance (all
resulting station clusters were examined taxa), mean H! diversity, 100 - %
by ANOVA and pair-wise multiple abundance of the two most numerically
comparison tests (Duncan’s test and dominant species, and two different
Tukey’s HSD) to help delineate the measures of % abundance of pollution-
major habitat types. Four site groups sensitive taxa.
resulted: oligohaline-mesohaline
stations (#8%) from all latitudes, Scoring criteria for each of these metrics
polyhaline-euhaline stations (>18%) were developed based on the
from northern latitudes (>34.5° N), distribution of values at undegraded
polyhaline-euhaline stations from sites: score of 1, if value of metric for
middle latitudes (30-34.5° N) and sample being evaluated was in the lower
polyhaline-euhaline stations from 10th percentile of corresponding
southern latitudes (<30° N). Seventy- reference-site values; score of 3, if value
five stations sampled during the 1994 of metric for sample was in the lower
survey were selected for the 10th-50th percentile of reference-site
development data set. These stations values; or score of 5, if value of metric
provided data from both degraded and for sample was in the upper 50th
undegraded sites in each of the four percentile of reference-site values.
habitats. Classification of stations into Scoring criteria were determined
degraded and undegraded categories separately for each metric and habitat
was based on the combination of type. A combined index value was then
chemical and toxicological criteria, computed for a sample by assigning a
mainly DO, and toxicity of sediment score for each component metric (based
bioassays. Marginal sites (minor on the individual scoring criteria for the
evidence of stress with toxicity in only corresponding habitat type) and then
one assay and no accompanying adverse averaging the individual scores. A
contaminant or DO conditions) were not combined score < 3 suggested the
included in the development data set. presence of a degraded benthic
assemblage (some apparent level of
Forty different infaunal attributes were stress to very unhealthy) given that its
tested with the 1994 development data condition, based on the averaged
set to determine those that best metrics, deviated from conditions
discriminated between undegraded and typical of the "best" (upper 50th
degraded sites within each habitat. This percentile) reference sites.
initial list of attributes included various
measures of diversity, abundance, Forty different combinations of the six
dominance, and presence of indicator candidate benthic metrics were further
species (e.g., pollution-sensitive vs. evaluated to determine which
pollution-tolerant species, surface vs. represented the best combined index.
subsurface feeders). A subset of six The metric combination that produced
candidate metrics was identified for the highest percentage of correct
possible inclusion in the index. Key classifications; i.e., agreement with
criteria considered in the selection were predictions of sediment bioeffects based
whether differences were in the right on the chemistry and toxicity data, was
direction and statistically significant then selected to represent the final
(based on results of Student t-tests, index. The resulting final index was the
Mann-Whitney U-tests, and average score of four metrics: (1) mean
Komogorov-Smirnov two-sample tests; abundance, (2) mean number of taxa, (3)
13-60 Case Studies

100 - % abundance of the top two percentage of samples where bioeffects
numerical dominants, and (4) % were expected (based on sediment
abundance of pollution-sensitive taxa quality guideline exceedances) than did
(i.e., percent of total faunal abundance any of the four individual sediment
represented by Ampeliscidae + bioassays (Fig. 13-16a) or individual
Haustoriidae + Hesionidae + Tellinidae infaunal attributes (Fig. 13-16b). Benthic
+ Lucinidae + Cirratulidae + Cyathura index values for base stations sampled
polita + C. burbanki. The final combined in 1995 covered the full scale from 1 to 5.
index correctly classified 93% of the Values < 1.5 (clearest evidence of a
stations province-wide in the degraded benthos) occurred at 14 of the
development data set and 75% of the 86 base sites, which represented 21% of
stations in the independent validation the province area (Fig.13-17).
data set. Transitional values of 2 to 2.5
(suggestive of some possible stress)
13.7.4 Results occurred at an additional 14 sites,
representing another 15% of the
The multimetric index of biotic integrity province. Values $3 (suggestive of an
index — consisting of measures of undegraded benthos) occurred at the
abundance, number of species, remaining 58 base sites, representing
dominance, and relative abundance of 64% of the area of the province.
pollution-sensitive taxa — produced a
high percentage of correct station By estuarine class, the estimated
classifications; i.e., agreement with percentage of area with degraded
predictions of sediment bioeffects based benthic assemblages was the highest for
on chemistry and toxicity data, in large tidal rivers and the lowest for large
comparison to other metric estuaries (Fig. 13-18). By subregion, this
combinations that were tested. The percentage was the highest in Florida
index correctly classified stations estuaries and the lowest in South
province-wide 93% of the time in the Carolina/Georgia estuaries.
1994 development data set and 75% of
the time in the independent 1993/1995 Extracted or summarized from the
validation data set. EMAP Carolinian Province Report,
Annual Statistical Summary for the 1995
Figure 13-15 illustrates that stations with EMAP - Estuaries Demonstration Project
index values below 3 (suggestive of in the Carolinian Province (Hyland et al.
some apparent stress to highly degraded 1998).
conditions) usually coincided with sites
considered to be degraded based on a Primary Contact: Jeffrey L. Hyland,
combination of chemistry and toxicity Carolinian Province Office,
data, and that stations with scores of 3 NOAA/National Ocean Service
or higher usually coincided with 217 Fort Johnson Rd. (P.O. Box 12559),
undegraded sites. Agreement is the Charleston, SC 29422-2559
highest at the two ends of the scale. 843-762-5415
Thus, the evaluation of sediment [email protected]
quality based on the benthic index
appears to agree reasonably well with
predictions of sediment bioeffects based
on the combined exposure data.
Additional comparisons revealed that
the benthic index detected a higher
Figure 13-15
Frequency distribution
of index scores for
undegraded vs.
degraded stations in
1993/1995
“development” data
set.
13-62 Case Studies

Figure 13-16
Comparison of
the percent of
expected
bioeffects
detected with the
benthic index vs.
(A) four sediment
bioassays and
(B) three
individual
infaunal
attributes.
a
Percent
expected
bioeffects - #
stations (1995
core &
supplemental)
where an effect
was detected / #
stations with $ 1
ER-M/PEL or $ 3
ER-L/TEL
exceedance.
Figure 13-17
Percent area
(and 95% C.I.) of
CP estuaries with
high ( 3),
intermediate (>
1.5 to < 3), and
low ( 1.5)
benthic index
values.
Figure 13-18
Comparison of
benthic index
values by
estuarine class
and subregion.
13-64 Case Studies

13.8 Assessment of the additional part of the study, trends in
fish communities structure were
Ecological Condition of assessed by collecting monthly beach
the Delaware and seine and trawl measurements during
Maryland Coastal Bays the summer at about 70 sites where
historic measurements of fish
13.8.1 Background communities have been made.
The coastal bays formed by the barrier 13.8.2 Methods

islands of Maryland and Delaware are
important ecological and economic Sampling sites were selected using a
resources whose physical characteristics stratified random sampling design in
and location make them particularly which the coastal bays were stratified
vulnerable to the effects of pollutants. A into several subsystems for which
first step in developing management independent estimates of condition were
strategies for these systems is to desired:
characterize their present condition and
how it has changed over time. This < Upper Indian River;
project was undertaken as a
collaborative effort of the Coastal Bays < Trappe Creek/Newport Bay;
Joint Assessment (CBJA), a group of
state and federal agencies, to assess the < St. Martin River;
ecological condition of this system and
fill a data void identified in previous < Artificial lagoons throughout the
characterization studies. coastal bays;
Two hundred sites were sampled in the < All remaining areas within
summer of 1993 using a probability- Maryland’s coastal bays; and
based sampling design that was
stratified to allow assessments of the < All remaining areas within
coastal bays as a whole, each of four Delaware’s coastal bays.
major subsystems within coastal bays
(Rehoboth Bay, Indian River Bay, The upper Indian River, Trappe Creek,
Assawoman Bay, and Chincoteague and St. Martin River were defined as
Bay) and four target areas of special sampling strata because resource
interest to resource managers (upper managers expressed particular concern
Indian River, St. Martin River, Trappe about these areas. Water quality data
Creek, and artificial lagoons). Measures suggest that each of these tidal creeks is
of biological response, sediment subject to excessive nutrient enrichment,
contaminants, and eutrophication were algal blooms, and low concentrations of
collected at each site using the same DO. These creeks are also believed to
sampling methodologies and quality transmit large nutrient loads (from
assurance/quality control procedures agricultural runoff) downstream
used by EMAP. The consistency of the contributing to eutrophication
sampling design and methodologies throughout the coastal bays (Boynton et
between this study and EMAP allows al. 1993).
unbiased comparison of conditions in
the coastal bays with that in other major Artificial lagoons were defined as a
estuarine systems in USEPA Region III stratum because of their high potential
that are sampled by EMAP. As an for impact based on their physical
characteristics and their proximity to a All sampling was conducted between
variety of contaminant sources (Brenum July 12 and September 30, 1993.
1976). These dredged canal systems can Sampling was limited to a single index
form the aquatic equivalent of streets in period because available resources were
development parcels; they already insufficient to sample in all seasons.
encompass 105 linear miles and almost Late summer is the time during which
4% of the surface area of Delaware’s environmental stress on estuarine
inland bays. In general, these systems systems in the mid-Atlantic region is
are constructed as dead-end systems expected to be greatest owing to high
with little or no freshwater inflows for temperatures and low dilution flows
flushing. They are often dredged to a (Holland 1990). The sampling period
depth greater than the surrounding coincided with the period during which
waters, leaving a ledge that further EMAP sampled estuaries of the mid-
inhibits exchange with nearby waters Atlantic region; therefore, data collected
and leads to stagnant water in the in the coastal bays annually for EMAP
canals. The placement of these systems can be incorporated into estimates of
in relatively high density residential ecological condition generated from
areas increases the potential Coastal Bays Joint Assessment (CBJA)
contaminant input. Much of the data. That data can then contribute to
modified land-use in dredged canal continuing development and evaluation
systems extends to the edge of the of EMAP indicators.
bulkheaded waters, providing a ready
source of unfiltered runoff of lawn-care Measurements of physical
and pesticides. In many cases, the characteristics provide basic information
bulkhead and dock systems in these about the natural environment.
canal systems are built from treated Knowledge of the physical context in
lumber containing chromium, copper, which biological and chemical data are
and arsenic, providing another source of collected is important for interpreting
contaminants. results accurately because physical
characteristics of the environment
Four replicate bottom grabs were determine the distribution and species
collected from each station with a 0.04- composition of estuarine communities,
m2 Young grab sampler. Of the two particularly assemblages of benthic
hundred sites sampled, 25 were in each macroinvertebrates. Salinity, sediment
of the first four sampling strata and 50 type, and depth are all important
were in each of the last two. Sites were influences on benthic assemblages
selected by simple random sampling in (Snelgrove and Butman 1994, Holland et
all strata except artificial lagoons. The al. 1989). Sediment grain size also
randomly selected sites were chosen by affects the accumulation of
enhancing the base EMAP grid (Overton contaminants in sediments. Fine-
et al. 1990). A different level of grained sediments generally are more
enhancement was applied to each susceptible to contamination than sands
stratum to obtain the required number because of the greater surface area of
of samples. Sites in the artificial lagoons fine particles (Rhoads 1974, Plumb
were selected by developing a list frame 1981).
(of all existing lagoons), randomly
selecting 25 lagoons from that list, and Depth, silt-clay content of the sediment,
then randomly selecting a site within bottom salinity, temperature, and pH
each selected lagoon. were measured to describe the physical
conditions at sites in the coastal bays.
13-66 Case Studies

Sediment type was defined according to phosphorus (TDP), and particulate
silt-clay content (fraction less than 63-µ); nitrogen and phosphorus. Table 13-18
classifications were the same as those lists the core environmental parameters
used for EMAP. Biologically sampled at the various sites.
meaningful salinity classes were defined
according to a modified Venice System Estimating the percent of eutrophied
(Symposium on the Classification of area in the coastal bays requires
Brackish Waters 1958). identifying threshold levels for selected
indicators that define eutrophication.
Healthy aquatic ecosystems require clear While no such levels have been
water, acceptable concentrations of established for the coastal bays, the
dissolved oxygen, limited Chesapeake Bay Program has
concentrations of phytoplankton, and established thresholds for five water
appropriate concentrations of nutrients. quality parameters to define critical
Clear water is a critical requirement for habitat requirements for supporting
submerged aquatic vegetation (SAV), SAV in a polyhaline environment
which provides habitat for many other (Dennison et al. 1993); these thresholds
aquatic organisms (Dennison et al. were used for our assessment (Table 13-
1993). As large concentrations of 19). All but one of the SAV restoration
suspended sediment or algal blooms goal attributes were measured directly.
reduce water clarity, the amount of The light attenuation coefficient was
sunlight reaching SAV is diminished calculated from Secchi depth
and the plants fail to thrive; measurements.
consequently, critical habitat for crabs,
fish, and other aquatic organisms is lost Threshold values of sediment
(Dennison et al. 1993). Nutrient contaminants developed by Long and
enrichment causes excessive algal Morgan (1990) and updated by Long et
growth in the water column and on the al. (1995) were used to interpret
surfaces of plants. As bacteria concentrations of sediment
metabolize the excess algae, they deplete contaminants measured in the coastal
dissolved oxygen in the water column bays. Two values were identified for
and sediments causing hypoxia and, in each contaminant: an effects range-low
extreme cases, anoxia. (ER-L) value corresponding to
contaminant concentrations above
Water quality in the coastal bays of which biological effects begin to appear,
Delaware and Maryland was evaluated and an effects-range median (ER-M)
using classes of indicators: measures of concentration, above which biological
algal productivity, dissolved oxygen effects are probable. Only a subset of
(DO), water clarity, and nutrients. the contaminant samples collected for
Measures of algal biomass included the the CBJA were processed because of cost
concentrations of chlorophyll in the constraints; consequently, comparisons
water column and sediment, and were limited to the artificial lagoons and
phaeophytin. Secchi depth, total the coastal bays as a whole.
suspended solids (TSS), and turbidity
were measured to assess water clarity. Sediment samples for analysis of benthic
Nutrient measures included dissolved macroinvertebrates, silt-clay content,
inorganic nitrogen (DIN; nitrite, nitrate, benthic chlorophyll, and chemical
and ammonium), dissolved inorganic contaminants were collected using a
phosphorus (DIP), total dissolved 0.044-m2 , stainless steel, Young-modified
nitrogen (TDN), total dissolved VanVeen grab. Four measures of
Table 13-18. Environmental parameters for the Maryland/Delaware Coastal Bays.
Physical Parameters
Depth
% Silt/Clay content
Salinity
Tem perature
pH
W ater Qua lity Param eters
Chlorophyll a
Phaeophytin
Benth ic chlorophyll
DO (Dissolved Oxygen)
NO 2 (Nitrite)
NO 3 (Nitrate)
Am monium
TDN (Total Dissolved Nitrogen)
Orthop hos pha te
TDP (Total Dissolved Phosphorus)
TPN (Total Particulate Nitrogen)
TPP (Total Particulate Phosphorus)
TPC (Total Particulate Carbon)
Secch i Dep th
TSS (Total Suspended Solids)
Turbidity
Benthic Param eters
Abundance
Biomass
Num ber of Species
Shannon-W iener Index
EMAP Index
Table 13-19. Chesapeake Bay submerged aquatic vegetation habitat requirements for a polyhaline
environment (Dennison et al. 1993).
Parameter Critical Value
Light attenua tion coefficient (k d; m -1) 1.5

-1
Total suspended solids (mgL ) 15
Ch loro phyll a (µg /l) 15
Dissolved inorganic nitrogen (µM) 10
Dissolved inorganic phosphorus (µM) 0.67
13-68 Case Studies

biological response were used to The tributaries to the coastal bays are
evaluate the condition of benthic in poorer condition than the
assemblages in the coastal bays of mainstems of the major subsystems.
Delaware and Maryland: abundance, Previous studies have suggested that
biomass, diversity, and the EMAP the major tributaries to the system:
benthic index. Abundance and upper Indian River, St. Martin River,
biomass are measures of total and Trappe Creek are in poorer
biological activity at a location. The condition than the mainstem water
diversity of benthic organisms bodies. This study confirmed that
supported by the habitat at a location finding. The percentage of area
often is considered a measure of the containing degraded benthos was
relative “health” of the environment. generally two to three times greater in
Diversity was evaluated using the the tributaries compared to the rest of
number of species; i.e., species the coastal bays. The percent of area
richness, at a location and the with DO less than the state standard
Shannon-Wiener diversity index, of 5-ppm was three to seven times
which incorporates both species greater in the tributaries. More than
richness and evenness components. 70% of the area in upper Indian River
The EMAP benthic index integrates and St. Martin River and in the
measures of species diversity, artificial lagoons had chlorophyll a
composition, biomass, and abundance concentrations exceeding the SAV
into a single value that distinguishes restoration goals.
between sites of good or poor
ecological condition (Schimmel et al. Among these systems, Trappe Creek
1994). A value of 0 or less denotes a contained the sites in the worst
degraded site at which the structure of condition. Two sites in the upper
the benthic community is poor, and portion of Trappe Creek had
the number of species, abundance of concentrations of chlorophyll a
selected indicator species, and mean exceeding 350 µgL-1 ; algal blooms
biomass are small. were evident at each site. In addition,
daytime DO levels exceeding 14-ppm
13.8.3 Results/Conclusions were measured at both sites.
Although, supersaturated DO often
Major portions of the coastal bays occurs in hypereutrophic waterbodies
have degraded environmental quality. on warm, sunny days. However, it
EMAP’s benthic index measured 28% appears that degraded conditions in
of the area in the coastal bays had the Trappe Creek system are spatially
degraded benthic communities. At limited to Trappe Creek and have not
least one sediment contaminant spread to Newport Bay.
exceeding the Long et al. (1995) ER-L Undoubtedly, this results from the
concentration (threshold of initial low freshwater flow from this
biological concern) were found in 68% tributary compared to the other
of the area in the coastal bays. More tributaries.
than 75% of the area in the coastal
bays failed the Chesapeake Bay Moreover, the coastal bays are in as
Program’s Submerged Aquatic poor or worse condition than either
Vegetation (SAV) restoration goals, the Chesapeake or Delaware Bays
which are a combination of measures with respect to sediment contaminant
that integrate nutrient, chlorophyll, levels, water quality, and benthic
and water clarity parameters. macroinvertebrate community
condition. Based on comparison to relatively unchanged during the past
EMAP data collected between 1990- twenty years while that of similar
1993, the coastal bays were found to systems in Delaware have changed
have 68% chemical contamination in substantially. Fish communities of the
the sediments, a higher prevalence Maryland coastal bays are dominated
than either Chesapeake Bay or by Atlantic silversides, bay anchovy,
Delaware Bay. The total area in the Atlantic menhaden, and spot. This
coastal bays that had at least one community structure is similar to that
sediment contaminant exceeding the of the Delaware coastal bays 35 years
Long et al. (1995) ER-L concentration ago. The fish fauna in Delaware’s
was 50% higher than the spatial extent coastal bays has shifted toward
EMAP estimated for Chesapeake Bay species of the Family Cyprinodontidae
using identical methods, and 40% (e.g., killifish and sheepshead
higher, though not statistically minnow) which are more tolerant to
distinguishable, from what EMAP low oxygen stress, and extremes of
estimated for Delaware Bay. salinity and temperature.
Twenty-eight percent of the area in Primary Contact: Dr. Frederik W. Kutz

the coastal bays had degraded benthic U.S. EPA, Region III
communities as measured by EMAP’s Environmental Science Center
benthic index. This was significantly 701 Mapes Rd.
greater than the 16% EMAP estimated Fort Meade, MD 20755
for Delaware Bay using the same 410-305-2742
methods and same index, and [email protected]
statistically indistinguishable from the
26% estimated for the Chesapeake
Bay.
Nutrients were not measured by

EMAP and statistically unbiased
estimates of average concentrations
are unavailable for either Chesapeake
or Delaware Bays. The Chesapeake
Bay Program though, recently
estimated that about 75% of the area
in Chesapeake Bay meets SAV
Restoration Goals. This is more than
three times the percent of area
meeting SAV Restoration Goals in the
coastal bays. Even when the turbidity
and TSS components of the SAV
Restoration Goals (which are naturally
high in shallow systems), are ignored,
almost half of the area in the coastal
bays still fails the SAV Restoration
Goal estimates for nutrients and
chlorophyll.
The fish community structure in

Maryland’s coastal bays has remained
13-70 Case Studies

Glossary
A posteriori classification - a Bioconcentration - a process by which

classification based on the results of there is a net accumulation of a chemical
experimentation. directly from water into aquatic organisms
resulting from simultaneous uptake (e.g.,
A priori classification - a classification via gill or epithelial tissue) and
made prior to experimentation. elimination.
Aquatic community - an association of Biological assemblage - a group of

interacting populations of aquatic phylogenetically (e.g., fish) or ecologically
organisms in a given waterbody or (e.g., benthic macroinvertebrates) related
habitat. organisms that are part of an aquatic
community.
Aquatic life uses - a subset of designated
uses for high quality waters. As such, Biological assessment or Bioassessment -
they are in need of special protection so an evaluation of the condition of a
that characteristics of their resident biotic waterbody using biological surveys and
communities are identified and protected. other direct measures of the resident biota
of the surface waters, in conjunction with
Assemblage - an association of interacting biological criteria.
populations of organisms in a given
waterbody (e.g., fish assemblage or Biological criteria or Biocriteria -
benthic macroinvertebrate assemblage). guidelines or benchmarks adopted by
States to evaluate the relative biological
Attribute - physical and biological integrity of surface waters. Biocriteria are
characteristics of habitats which can be narrative expressions or numerical values
measured or described. that describe biological integrity of aquatic
communities inhabiting waters of a given
Benthic macroinvertebrates - see benthos. classification or designated aquatic life
use.
Benthos - animals without backbones,
living in or on the sediments, of a size Biological indicators - plant or animal
large enough to be seen by the unaided species or communities with a narrow
eye, and which can be retained by a U.S. range of environmental tolerances that
Standard No. 30 sieve (28 openings/in, may be selected for monitoring because
0.595-mm openings). Also referred to as their absence or presence and relative
benthic macroinvertebrates, infauna, or abundances serve as barometers of
macrobenthos. environmental conditions.
Bioaccumulation - a process by which Biological integrity - the condition of the

chemicals are taken up by aquatic aquatic community inhabiting unimpaired
organisms directly from water as well as waterbodies of a specified habitat as
through exposure via other routes, such as measured by community structure and
consumption of food and sediment function.
containing the chemicals.
Estuarine and Coastal Marine Waters: Bioassessment and Biocriteria Technical Guidance G-1
Biological monitoring or Biomonitoring - Discriminant analysis - a type of
multiple, routine biological surveys over multivariate analysis used to distinguish
time using consistent sampling and between two groups.
analysis methods for detection of changes
in biological condition. Ecological integrity - the condition of an
unimpaired ecosystem as measured by
Biological survey or Biosurvey - combined chemical, physical (including
collecting, processing and analyzing habitat), and biological attributes.
representative portions of an estuarine or
marine community to determine its Ecoregion - geographic regions of
structure and function. ecological similarity defined by similar
climate, landform, soil, natural vegetation,
Biomagnification - the result of the hydrology or other ecologically relevant
processes of bioconcentration and variables.
bioaccumulation by which tissue
concentrations of bioaccumulated Effects Range-Low - concentration of a
chemicals increase as the chemical passes chemical in sediment below which toxic
up through two or more trophic levels in effects were rarely observed among
the food chain. sensitive species (10th percentile of all toxic
effects).
Biota - plants, animals and other living
resources. Effects Range-Median - concentration of a
chemical in sediment above which toxic
Brackish - water with salt content ranging effects are frequently observed among
between that of sea water and fresh water; sensitive species (50th percentile of all toxic
commonly used to refer to oligohaline effects).
waters.
Epibenthos - those animals (usually
Coastal waters - marine waters adjacent to excluding fishes) living on the top of the
and receiving estuarine discharges and sediment surface.
extending seaward over the continental
shelf and/or the edge of the U.S. Epifauna - benthic animals living on the
territorial sea. sediment or on and among rocks and
other structures.
Community - any group of organisms
belonging to a number of different species Estuarine or coastal marine classes -
that co-occur in the same habitat or area; classes that reflect basic biological
an association of interacting assemblages communities and that are based on
in a given waterbody. physical parameters such as salinity,
depth, sediment grain size, dissolved
Demersal - living on or near the bottom of oxygen and basin geomorphology.
a body of water (e.g., mid-water and
bottom-dwelling fish and shellfish, as Estuarine waters - semi-enclosed body of
opposed to surface fish). water which has a free connection with
the open sea and within which seawater is
Designated uses - descriptions of the measurably diluted with fresh water
optimal use of each waterbody as defined derived from land drainage.
by States including natural fisheries,
recreation, transportation, or mixed uses. Facultative - capable of adaptive response
to varying environments.
G-2 Glossary
Habitat - a place where the physical and Indicator taxa or Indicator species - those
biological elements of ecosystems provide organisms whose presence (or absence) at
an environment and elements of the food, a site is indicative of specific
cover and space resources needed for environmental conditions.
plant and animal survival.
Infauna - see benthos.
Halocline - a vertical gradient in salinity.
In situ - measurements taken in the
Holoplankton - an aggregate of passively natural environment.
floating, drifting or somewhat motile
organisms throughout their entire life Kurtosis - a measure of the departure of a
cycle. frequency distribution from a normal
distribution, in terms of its relative
Hypoxia - the condition of low dissolved peakedness or flatness.
oxygen in aquatic systems (typically with
a concentration < 2-mgL-1 but > 0.5- Littoral zone - the intertidal zone of the
mgL-1 ). estuarine or seashore; i.e., the shore zone
between the highest and lowest tides.
IBI or Index of Biotic Integrity - a fish
community assessment approach that Macrobenthos - see benthos.
incorporates the zoogeographic,
ecosystem, community and population Macrofauna - animals of a size large
aspects of fisheries biology into a single enough to be seen by the unaided eye and
ecologically-based index of the quality of a which can be retained by a U.S. Standard
water resource. No. 30 sieve (28 meshes/in, 0.595-mm
openings).
Impact - a change in the chemical,
physical or biological quality or condition Macroinvertebrates - animals without
of a waterbody caused by external backbones of a size large enough to be
sources. seen by the unaided eye and which can be
retained by a U.S. Standard No. 30 sieve
Impairment - a detrimental effect on the (28 meshes/in, 0.595-mm openings).
biological integrity of a water body caused
by an impact. Macrophytes - large aquatic plants that
may be rooted, non-rooted, vascular or
Indexes - a usually dimensionless numeric algiform (such as kelp); including
combination of scores derived from submerged aquatic vegetation, emergent
biological measures called metrics. aquatic vegetation, and floating aquatic
vegetation.
Index period - a sampling period, with
selection based on temporal behavior of Meiofauna - small interstitial; i.e.,
the indicator(s) and the practical occurring between sediment particles,
considerations for sampling. animals that pass through a 1-mm mesh
sieve but are retained by a 0.1-mm mesh.
Indicator - characteristics for the
environment, both abiotic and biotic, that Meroplankton - organisms that are
can provide quantitative information on planktonic only during the larval stage of
environmental conditions. their life history.
Mesohaline - the estuarine salinity zone Photic zone - the region in a water body
with a salinity range of 5-18-ppt. extending from the surface to the depth of
light penetration.
Metric - a calculated term or enumeration
which represents some aspect of biological Plankton - free-floating or drifting
assemblage structure, function, or other organisms with movements determined
measurable characteristic of the biota that by the motion of the water.
changes in some predictable way in
response to impacts to the water body. Population - an aggregate of
interbreeding individuals of a biological
Multimetric approach - an analysis species within a specified location.
technique that uses a combination of
several measurable characteristics of the Pseudoreplication - the repeated
biological assemblage to provide an measurement of a single experimental unit
assessment of the status of water or sampling unit, with the treatment of the
resources. measurements as if they were
independent replicates of the sampling
Multivariate community analysis - unit.
statistical methods (e.g., ordination or
discriminant analysis) for analyzing Pycnocline - a zone of marked density
physical and biological community data gradient.
using multiple variables.
Reference condition - the chemical,
NPDES or National Pollutant Discharge physical or biological quality or condition
Elimination System - a permit program exhibited at either a single site or an
under Section 402 of the Clean Water Act aggregation of sites that represents the
that imposes discharge limitations on least impaired condition of a classification
point sources by basing them on the of waters to which the reference condition
effluent limitation capabilities of a control applies.
technology or on local water quality
standards. Reference sites - minimally impaired
locations in similar water bodies and
Oligohaline - the estuarine salinity zone habitat types at which data are collected
with a salinity range of 0.5-5-ppt. for comparison with test sites. A separate
set of reference sites are defined for each
Optimal - most favorable point, degree, or estuarine or coastal marine class.
amount of something for obtaining a
given result; in ecology most natural or Replicate - taking more than one sample
minimally disturbed sites. or performing more than one analysis.
Pelagic - pertaining to open waters or the Saprobien system - an ecological

organisms which inhabit those waters. classification of a polluted aquatic system
that is undergoing self-purification.
Pelagic zone - the area of open water Classification is based on relative levels of
beyond the littoral zone. pollution, oxygen concentration and types
of indicator microorganisms; i.e.,
Percent fines - in analysis of sediment saprophagic microorganisms – feeding on
grain size, the percent of fine (.062-mm) dead or decaying organic matter.
grained fraction of sediment in a sample.
G-4 Glossary
Seiche - a wave that oscillates (for a
period of a few minutes to hours) in lakes,
bays, lagoons or gulfs as a result of
seismic or atmospheric disturbances (e.g.,
"wind tides").
Simulation models - mathematical

models (logical constructs following from
first principles and assumptions),
statistical models (built from observed
relationships between variables), or a
combination of the two.
Skewness - the degree of statistical

asymmetry (or departure from symmetry)
of a population. Positive or negative
skewness indicates the presence of a long,
thin tail on the right or left of a
distribution respectively.
Test sites - those sites being tested for

biological impairment.
Trophic level - a broad class of an

ecosystem (e.g., green plants, herbivores,
carnivores) in which all organisms
procure food in the same general manner.
Use designations - predominant uses each

State determines appropriate for a
particular estuary, region, or area within
the class.
Zooplankton - free-floating or drifting

animals with movements determined by
the motion of the water.
Literature Cited
Alden, R.W., S.B. Weisberg, J.A. American Public Health Association

Ranasinghe, and D.M. Dauer. 1997. (APHA). 1981. Standard methods for the
Optimizing temporal sampling examination of water and wastewater.
strategies for benthic environmental American Public Health Association,
monitoring programs. Marine Pollution American Water Works Association, and
Bulletin 34(11):913-922. Water Pollution Control Federation.
15th edition, Washington, DC.
Allen, M.J. and R.W. Smith. 2000.
Development of demersal fish biointegrity American Society for Testing and
indices for coastal Southern California. Materials (ASTM). 1998a. Standard
Southern California Coastal Water guide for conducting 10-day static
Research Project, Westminster, CA. sediment toxicity tests with marine and
estuarine amphipods. E1367-92.
Allen, M.J., D. Diener, J. Mubarak, S.B. Volume 11.05:732-757. Annual Book of
Weisberg, and S.L. Moore. 1999. Standards: American Society of Testing and
Megabenthic invertebrate assemblages Materials, Conshohocken, PA.
of the mainland shelf of southern
California in 1994. Pages 113-124 in American Society for Testing and
Weisberg, S.B. and D. Hallock (editors). Materials (ASTM). 1998b. Standard
Southern California Coastal Water Research guide for collection, storage,
Project, Annual Report 1997-1998. characterization, and manipulation of
Reynolds and Reynolds, Santa Ana, CA. sediments for toxicological testing.
E1391-94. Volume 11.05:768-788. Annual
Allen, H.E., G. Fu and B. Deng. 1993. Book of Standards: American Society of
Analysis of acid-volatile sulfide (AVS) Testing and Materials, Conshohocken,
and simultaneously extracted metals PA.
(SEM) for the estimation of potential
toxicity in aquatic sediments. American Society for Testing and
Environmental Toxicology and Chemistry Materials (ASTM). 1998c. Standard
12:1441-1453. guide for conducting sediment toxicity
tests with marine and estuarine
Alve, E. 1991. Foraminifera, climatic polychaetous annelids. E1611-94.
change, and pollution: A study of late Volume 11.05:1009-1032. Annual Book of
Holocene sediments in Drammensfjord, Standards: American Society of Testing and
southeast Norway. The Holocene Materials, Conshohocken, PA.
1(3):243-261.
American Society for Testing and
American Public Health Association Materials (ASTM). 1991. Standard
(APHA). 1992. Standard methods for the guide for collection, storage,
examination of waters and wastewater. characterization, and manipulation of
American Public Health Association, sediments for toxicological testing.
American Water Works Association, and ASTM Designation E1391-90. Annual
Water Pollution Control Federation. Book of Standards. American Society for
18th edition, Washington, DC. Testing and Materials, Philadelphia, PA.
Estuarine and Coastal Marine Waters: Bioassessment and Biocriteria Technical Guidance L-1
Ankley, G.T., D.M. DiToro, D.J. Hansen Resource Planning and Decision Making.
and W.J. Berry. 1996. Technical basis Lewis Publishers. Boca Raton, FL.
and proposal for deriving sediment
quality criteria for metals. Environmental Barbour, M.T., J.L. Plafkin, B.P. Bradley,
Toxicology and Chemistry 15(12):2056- C.G. Graves, and R.W. Wisseman. 1992.
2066. Evaluation of EPA's rapid bioassessment
benthic metrics: Metric redundancy and
Ankley, G., M. Schubauer-Berigan, J. variability among reference stream sites.
Dierkes. 1991. Predicting the toxicity of Environmental Toxicology and Chemistry
bulk sediments to aquatic organisms 11:437-449.
with aqueous test fractions: pore water
vs. elutriate. Environmental Toxicology Barss, M.S. and G.L. Williams. 1973.
and Chemistry 10:925-939. Palynology and nannofossil processing
techniques. Geological Survey of Canaca
Association of Bay Area Governments Paper. 73-26, 1-25.
(ABAG). 1991. Status and trends report
on wetlands and related habitats in the San Batiuk, R.A., R.J. Orth, K.A. Moore, W.C.
Francisco estuary. San Francisco Estuary Dennison, J.C. Stevenson, L.W. Staver,
Project. Oakland, CA. V. Carter, N.B. Rybicki, R.E. Hickman, S.
Kollar, S. Bieber, P. Heasly. 1992.
Barbour, M.T., J. Gerritsen, B.D. Snyder, Chesapeake Bay Submerged Aquatic
J.B. Stribling. 1999. Rapid bioassessment Vegetation Habitat Requirements and
protocols for use in streams and wadeable Restoration Targets: A Technical Synthesis.
rivers: periphyton, benthic Chesapeake Bay Program, 68-WO-0043.
macroinvertebrates, and fish, 2nd ed. EPA
841-B-99-002. U.S. Environmental Bergen, M., S.B. Weisberg, R.W. Smith,
Protection Agency, Office of Water, D. Cadien, A. Dalkey, D. Montagne, J.K.
Washington, D.C. Stull, R.G. Velarde. 1999. Relationship
between depth, latitude, and sediment
Barbour, M.T., J. Gerritsen, and J.S. and the structure of benthic infaunal
White. 1996a. Development of the Stream assemblages on the mainland shelf of
Condition Index (SCI) for Florida. southern California. Pages 125-136 in
Prepared for FL DEP, Tallahassee, FL. Weisberg, S.B. and D. Hallock (editors).
Southern California Coastal Water Research
Barbour, M.T., J.M. Diamond, C.O. Project, Annual Report 1997-1998.
Yoder. 1996b. Biological assessment Reynolds and Reynolds, Santa Ana, CA.
strategies: Applications and limitations.
Pages 245-270 in D.R. Grothe, K.L. Bernstein, B.B., B.E Thompson, and R.W.
Dickson, and D.K. Reed-Judkins Smith. 1991. A combined science and
(editors). Whole effluent toxicity testing: management framework for developing
An evaluation of methods and prediction of regional monitoring objectives. Presented
receiving system impacts. SETAC Press, at the National Estuary Program Science
Pensacola, Florida. Symposium, Sarasota, FL. 25-27
February 1991.
Barbour, M.T., J.B. Stribling, and J.R.
Karr. 1995. The multimetric approach Bilyard, G.R. 1987. The value of benthic
for establishing biocriteria and infauna in marine pollution monitoring
measuring biological condition. In W. studies. Marine Pollution Bulletin 18:581-
Davis, T. Simon (editors). Biological 585.
Assessment and Criteria: Tools for Water
L-2 Literature Cited

Blalock, H.M., Sr. 1979. Social Statistics. Boynton, W.R., W.M. Kemp, J. Garber,
Revised 2nd edition. McGraw-Hill Book J.M. Barnes, L.L. Robertson, and J.L.
Company, New York, NY. Watts. 1988. Chesapeake Bay water quality
monitoring program ecosystems processes
Boesch, D.F. 1977. Application of component. Level 1 Report No. 5.
numerical classification in ecological Prepared for Maryland Department of
investigations of water pollution. EPA Environment by University of Maryland
Grant No. R803599-01-1, ROAP/TASK Center for Environmental and Estuarine
No. 21 BEI, U.S. EPA Corvallis Studies.
Environmental Research Laboratory,
Newport, OR. 115 p. Brenum, G. 1976. A comparative study of
benthic communities of dredged lagoons,
Bowman, M.L., E. Dohner, and C. tidal creeks, and areas of open bays in Little
Dohner. 1993. Summary of estuarine Assawoman, Indian River, and Rehoboth
monitoring program attributes for: Bays, Delaware. M.S. thesis, College of
Chesapeake Bay benthos; Chesapeake Bay Marine Studies, University of Delaware,
plankton; Tar/Pamlico; EMAP-Estuaries Newark, DE.
Virginian Province demonstration project;
Naples Bay, Florida; San Francisco estuary Brumbaugh, W., C. Ingersoll, N.
and wetlands; Puget Sound ambient Kemble, T. May, and J. Zajicek. 1994.
monitoring program; and Puget Sound Chemical characterization of sediments
estuary program. Prepared for U.S. and pore water from the Upper Clark
Environmental Protection Agency, Fork River and Milltown Reservoir,
Assessment and Watershed Protection Montana. Environmental Toxicology and
Division, Oceans and Coastal Protection Chemistry 13:1971-1973.
Division, and Health and Ecological
Criteria Division, Washington, DC by Brush, G.S. 1989. Rates and patterns of
Tetra Tech, Inc., Owings Mills, MD. estuarine sediment accumulation.
Limnology and Oceanography 34(7):1235-
Boyle, T.P., G.M. Smillie, J.C. Anderson, 1246.
and D.R. Bieson. 1990. A sensitivity
analysis of nine diversity and seven Bufflap, W. and H. Allen. 1995.
similarity indices. Research Journal of the Sediment pore water collection methods:
Water Pollution Control Federation 62:749. A review. Water Research 29:165-177.
Boynton, W.R., J.H. Garber, R. Summers, Bulger, A.J., B.P. Hayden, M.E. Monaco,
and W.M. Kemp. 1995. Inputs, D.M. Nelson, and M.G. McCormick-Ray.
transformations, and transport of 1993. Biologically-based estuarine
nitrogen and phosphorus in Chesapeake salinity zones derived from a
Bay and selected tributaries. Estuaries multivariate analysis. Estuaries
18(1B):285-314. 16(2):311-322.
Boynton, W.R., L. Murray, W.M. Kemp, Burgess, R., K. Schweitzer, R. McKinney,

J.D. Hagy, C. Stokes, F. Jacobs, J. Bowers, D. Phelps. 1993. Contaminated marine
S. Souza, B. Rinsky, and J. Seibel. 1993. sediments: Water column and
Maryland’s Coastal Bays: An assessment of interstitial toxic effects. Environmental
aquatic ecosystems, pollutant loadings, and Toxicology and Chemistry 12:127-138.
management options. Prepared for
Maryland Department of the Carmichael, J.T., B.M. Richardson, M.
Environment. Roberts, and S.J. Jordan. 1992. Fish
assemblages and dissolved oxygen trends in Quantitative inferences using biotic
eight Chesapeake Bay tributaries during the remains in the sediment record.
summers of 1989-1991: a data report. Advances in Chemistry 237:1-51.
Maryland Department of Natural
Resources, Chesapeake Bay Research Christian, R.R. 1989. Microbial ecology
and Monitoring Division, Annapolis, and organic detritus in estuaries. In
MD. J.W. Day, Jr., C.A.S. Hall, W.M. Kemp,
and A. Yanez-Arancibia (editors).
Carriker, M.R. 1967. Ecology of Estuarine Ecology. John Wiley & Sons,
estuarine benthic invertebrates: A New York, NY. pp. 558.
perspective. American Association for
the Advancement of Science, Cochran, W.G. 1963. Sampling
Washington, DC. Estuaries 83:442-487. Techniques. John Wiley and Sons, Inc.,
New York, NY.
Chaloud, D.J. and D.V. Peck, editors.
1994. Environmental Monitoring and Conley, D.J., C.L. Shelske and E.F.
Assessment Program: Integrated Quality Stoermer. 1993. Modification of the
Assurance Project Plan for the Surface biogeochemical cycle of silica with
Waters Resource Group, 1994 Activities. eutrophication. Marine Ecological
EPA 600/X-91/080, Rev. 2.00. USEPA, Progress Series 101:179-192.
Las Vegas, NV.
Conover, W.J. 1980. Practical
Chapman, P.M. 1996. Presentation and Nonparametric Statistics. 2nd edition. John
interpretation of sediment quality triad Wiley and Sons, Inc., New York, NY.
data. Ecotoxicology 5:327-339.
Conquest, L.L., S.C. Ralph, and R.J.
Chapman, P.M. 1988. Marine sediment Naiman. 1994. Implementation of
toxicity tests. In J.J. Lichtenberg, F.A. large-scale stream monitoring efforts:
Winter, C.I. Weber, and L. Fredkin Sampling design and data analysis
(editors). Chemical and Biological issues. Pages 69-90 in L. Loeb and A.
Characterization of Sludges, Sediments, Spacie (editors). Biological Monitoring of
Dredge Spoils, and Drilling Muds. Aquatic Systems. Lewis Publishers, Boca
Philadelphia, PA: ASTM. Raton, FL.
Chapman, P.M., R.N. Dexter, and E.R. Cooper, S.R. 1995. Chesapeake Bay
Long. 1987. Synoptic measures of watershed historical land use: Impact
sediment contamination, toxicity, and on water quality and diatom
infaunal community structure (the communities. Ecological Applications
Sediment Quality Triad). Marine Ecology 5:703-723.
Progress Series 37:75-96.
Cooper, S.R. and G.S. Brush. 1991.
Charles et al. 1994. Paleolimnological Long-term history of Chesapeake Bay
approaches to biological monitoring. anoxia. Science 254:992-996.
Pages 233-293 in L.L. Loeb, and A.
Spacie (editors). Biological monitoring of Correll, D.L. 1987. Nutrients in
aquatic systems. CRC Press, Boca Raton, Chesapeake Bay. Pages 298-320 in S.K.
FL. Majumdar, L.W. Hall, Jr. and H.M.
Austin (editors). Contaminant Problems
Charles, D.F. and J.P. Smol. 1994. Long- and Management of Living Chesapeake Bay
term chemical changes in lakes:

Resources. Pennsylvania Academy of Dennison, W.C., R.J. Orth, K.A. Moore,
Science. J.C. Stevenson, V. Carter, S. Kollar, P.
Bergstrom, and R.A. Batiuk. 1993.
Costanza, R., S.O. Funtowicz, and J.R. Assessing water quality with submerged
Ravetz. 1992. Assessing and aquatic vegetation. Bioscience 43:86-94.
communicating data quality in policy-
relevant research. Environmental Diaz, R. and W. Nelson. 1993. Middle
Management 16(1):121-131. and southern Atlantic coast estuarine
benthic invertebrate metrics development.
Dale, B., T.A. Thorsen and A. Fjellsa. A Proceedings: Estuarine and Near
1999. Dinoflagellate cysts as indicators Coastal Bioassessment and Biocriteria
of cultural eutrophication in the Workshop, (November 18-19, 1992.)
Oslofjord, Norway. Estuarine, Coastal Annapolis, Maryland. U.S.
and Shelf Science 48:371-382. Environmental Protection Agency,
Office of Science and Technology.
Dardeau, M.R., R.F. Madlin, W.W. Washington, DC.
Schroeder, and J.P. Stout. 1992.
Estuaries: Biodiversity of the southeastern Dickerson, R. 1995. Atmospheric
United States. C.T. Hackney, S.M. nitrogen deposition to the Chesapeake
Adams, and W.H. Martin (editors). John Bay. In P. Hill and S. Nelson (editors).
Wiley & Sons, New York, NY. pp. 779. Toward a Sustainable Coastal Watershed:
The Chesapeake Experiment. Proceedings of
Dauer, D.M. 1993. Biological criteria, a Conference, 1-3 June 1994, Norfolk, VA.
environmental health and estuarine Chesapeake Research Consortium,
macrobenthic community structure. Edgewater, MD. CRC Publication No.
Marine Pollution Bulletin 26:249-257. 149. p. 507.
Davies, S.P., L.T. Somides, D.L. DiToro, D.M., J.D. Mahony, D.J. Hansen,
Courtemanch, and F. Drummond. 1993. K.J. Scott, M.B. Hinks, S.M. Mayr and
Maine Biological Monitoring and Biocriteria M.S. Redmond. 1990. Toxicity of
Development Program. Maine cadmium in sediments: The role of acid
Department of Environmental volatile sulfides. Environmental
Protection, Bureau of Water Quality Toxicology and Chemistry 9:1487-1502.
Control, Division of Environmental
Evaluation and Lake Studies, Augusta, DiToro, D.M., C. Zarba, D.J. Hansen,
ME. R.C. Swartz, C.E. Cowan, H.E. Allen,
N.A. Thomas, P.R. Paquin and W.J.
Day, J.W., C.A.S. Hall, W.M. Kemp, and Berry. 1991. Technical basis for
A. Yanez-Aranciba. 1989. Estuarine establishing sediment quality criteria for
Ecology. John Wiley & Sons, New York, non-ionic organic chemicals using
NY. 558 pp. equilibrium partitioning. Environmental
Toxicology and Chemistry 10:1299-1307.
Deegan, L.A., J.T. Finn, S.G. Ayvazian,
C.A. Ryder-Kieffer, and J. Buonaccorsi. Dixit, S.S., J.P. Smol, J.C. Kingston, D.F.
1997. Development and Validation of an Charles. 1992. Diatoms: powerful
Estuarine Biotic Integrity Index. indicators of environmental change.
Estuaries 20:601-617. Environmental Science and Technology
26(1):23-32.
Delaware Chamber of Commerce,
personal communication, 1990.
Dossis, P. and L.J. Warren. 1981. Zinc assessment of demersal fauna
and lead in background and (macroinvertebrates and fishes): Pilot Study
contaminated sediments from Spencer in Puget Sound, Washington. Final report
Gulf, South Australia. Environmental to USEPA, Washington, DC.
Science and Technology 15:1451-6.
Eaton, L. 1994. Results of a test of three
Dycus, D.L. 1995. Aquatic ecological Methods, February 7, 1994. North
health determinations for TVA reservoirs - Carolina Division of Environmental
1994. An informal summary of 1994 vital Management Biological Assessment
monitoring results and ecological health Group. Memorandum to Ken Eagleson,
determination methods. Tennessee Valley May 10, 1994.
Authority Water Management.
Eaton, L. 1992a. Pamlico basin sampling:
Dycus, D.L. and D.L. Meinert. 1993. More metal hotspots. Memorandum
Monitoring and evaluation of aquatic dated March 11, 1992 to T. MacPherson,
resource health and use suitability in North Carolina Department of
Tennessee Valley Authority reservoirs. Environment, Health, and Natural
Water Management. Draft. Resources, Division of Environmental
Management, Raleigh, NC.
Eaton, C.M. 1997. Sediment wet-sieving
technique to determine "percent fines." Eaton, L. 1992b. Diaz method testing
C.M. Eaton, Bio-Marine Enterprises, results. Memorandum date March 30,
Seattle, WA. Fax transmission to M. 1992 to Ken Eagleson, North Carolina
Bowman, Tetra Tech, Inc., Owings Mills, Department of Environment, Health,
MD. 4 February 1997. and Natural Resources, Division of
Environmental Management, Raleigh,
Eaton, C. M. 1995. Population patterns NC.
of demersal fauna and environmental
stress: a preliminary, trawl-based Eaton, L. 1992c. Biological results from
assessment. Puget Sound Notes 36:1-6. sediment toxicity survey, Neuse and
Pamlico estuaries, January 9-10, 1992.
Eaton, C.M. 1994. Development of trawl- Memorandum dated April 14, 1992 to
based tools for the quantitative assessment of Harold Quidley, North Carolina.
demersal fauna (macroinvertebrates and Department of Environment, Health,
fishes): A summary of phase I and II. Final and Natural Resources, Division of
Report to USEPA, Washington, DC. Environmental Management, Raleigh,
Order No. 4642. NC.
Eaton, C.M. and P.A. Dinnel. 1994. Eaton, L. 1992d. Letter dated
Development of trawl-based criteria for the September 9, 1992 from L. Eaton, North
assessment of demersal fauna Carolina Department of Environment,
(macroinvertebrates and fishes): Pilot study Health, and Natural Resources, Division
in Puget Sound, Washington. Presented at of Environmental Management, Raleigh,
Estuarine and Near Coastal Marine NC, to M. Bowman, Tetra Tech, Inc.,
Bioassessment/ Biocriteria Workgroup Owings Mills, MD.
Meeting. USEPA, Baltimore, MD.
January 6th. Engle, V.D. and J.K. Summers. 1999.
Refinement, validation, and application
Eaton, C.M. and P.A. Dinnel. 1993. of a benthic condition index for northern
Development of trawl-based criteria for

Gulf of Mexico estuaries. Estuaries Ferraro, S.P. and F.A. Cole. 1995.
22:624-635. Taxonomic level sufficient for assessing
pollution impacts on the southern
Engle, V.D., J.K. Summers, and G.R. California bight macrobenthos -
Gaston. 1994. A benthic index of revisited. Environmental Toxicology and
environmental condition of Gulf of Chemistry 14(6):1031-1040.
Mexico estuaries. Estuaries 17(2):372-
384. Ferraro, S.P., F.A. Cole, W.A. DeBen,
and R.C. Swartz. 1989. Power-cost
Fairweather, P.G. 1991. Statistical efficiency of eight macrobenthic
power and design requirements for sampling schemes in Puget Sound,
environmental monitoring. Australian Washington, USA. Canadian Journal of
Journal of Marine Freshwater Research Fisheries and Aquatic Sciences 46(10):2157-
42:555-67. 2165.
Farrell, D.H. 1993a. A community based Ferraro, S.P., R.C. Swartz, F.A. Cole, and
metric for marine benthos (Draft). Florida W.A. DeBen. 1994. Optimum
Department of Environmental macrobenthic sampling protocol for
Protection, Tampa, FL. detecting pollution impacts in the
southern California Bight.
Farrell, D. H. 1993b. Bioassessment in Environmental Monitoring and Assessment
Florida. Pages 17-26 in A Proceedings: (29):127-153.
Estuarine and Near Coastal
Bioassessment and Biocriteria Flannagan, J.F. 1970. Efficiencies of
Workshop, Annapolis, MD. USEPA, various grabs and corers in sampling
Office of Science and Technology, freshwater benthos. Journal of the
Washington, D.C. Fisheries Research Board of Canada
27:1631-1700.
Ferguson, R.L. and L.L. Wood. 1994.
Rooted vascular aquatic beds in the Flint, R.W. and R.D. Kalke. 1985.
Albemarle-Pamlico estuarine system. Benthos Structure and function in a
National Marine Fisheries Service, south Texas estuary. Contributions in
Beaufort, NC. Project No. 94-02. Marine Science 28:33-53.
Ferraro, S.P. and F.A. Cole. 1990. Forstner, U. and G.T.W. Wittmann.
Taxonomic level and sample site 1981. Metal pollution in the aquatic
sufficient for assessing pollution impacts environment. Second revised edition.
on the southern California Springer-Verlag, New York, NY.
macrobenthos. Marine Ecology Progress
Series 67:251-262. Fredette, T.J., D.A. Nelson, T. Miller-
Way, J.A. Adair, V.A. Sotler, J.E.
Ferraro, S.P. and F.A. Cole. 1992. Clausner, E.B. Hands, and F.J. Anders.
Taxonomic level sufficient for assessing 1989. Selected tools and techniques for
a moderate impact on macrobenthic physical and biological monitoring of
communities in Puget Sound, aquatic dredged material disposal sites.
Washington, D.C. Canadian Journal of Final Report. U.S. Army Engineer
Fisheries and Aquatic Sciences 49(b):1184- Waterways Experiment Station,
1188. Vicksburg, MS.
Frydenborg R. 1994. Lake bioassessments Green, R.H. 1984. Some guidelines for
for the determination of nonpoint source the design of biological monitoring
impairment in Florida. Draft. FL DEP, programs in the marine environment.
Biology Section, Division of Pages 233-245 in H.H. White (editor).
Administrative and Technical Services, Concepts of Marine Pollution
Tallahassee, FL. July. Measurements. University of Maryland
Sea Grant, College Park, MD.
Gaston, G.R., D.L. Lee, and J.C. Nasci.
1988. Estuarine macrobenthos in Guillen, G. 1995a. Development of a rapid
Calcasieu Lake, Louisiana: Community bioassessment method and index of biotic
and trophic structure. Estuaries 11:192- integrity in southeast Texas. Presented at
200. Estuarine and Near Coastal Marine
Bioassessment/Biocriteria Workgroup
Gibson, G.R. 1995. Near coastal marine Meeting. U.S. EPA, Baltimore, MD.
waters pilot project (unpublished report). January 6th.
USEPA, Office of Science and
Technology, Health and Ecological Guillen, G.J. 1995b. Development of a
Criteria Division, Washington, DC. Rapid Bioassessment method and index of
biotic integrity for coastal environments
Gibson, G.R. et al. 1993. Proceedings located along the northwest Gulf of Mexico -
Estuarine and Near Coastal Marine DRAFT. Texas National Resource
Bioassessment and Biocriteria Workshop, Conservation Commission,
18-19. November, 1992. Environmental Assessment Program,
Field Operations Division.
Gibson, G.R. 1992. Procedures for
initiating narrative biological criteria. Guillen, G. 1994. Development of a rapid
EPA-822-B-92-002. USEPA, Office of bioassessment method and index of biotic
Science and Technology, Washington, integrity in southeast Texas. Presented at
DC. Estuarine and Near Coastal Marine
Bioassessment/Biocriteria Workgroup
Gilbert, R.O. 1987. Statistical Methods for Meeting. USEPA, Baltimore, MD.
Environmental Pollution Monitoring. Van
Nostrand Reinhold, New York. 320pp. Hansen, D.J., Berry, W.J., Mahony, J.D.,
Boothman, W.S., DiToro, D.M., Robson,
Glew, J.R. 1988. A portable extruding D.L., Ankley, G.T., Ma, D., Yan, Q.,
device for close interval sectioning of Pesch, C.E. 1996. Predicting the toxicity
unconsolidated core samples. Journal of of metal-contaminated field sediments
Paleolimnology 1:235-239. using interstitial concentration of metals
and acid-volatile sulfide normalizations.
Goodyear, C.P. 1985. Relationship Environmental Toxicology and Chemistry
between reported commercial landings 15:(12) 2080-2094.
and abundance of striped bass in
Chesapeake Bay, Maryland. Transactions Helsel, D.R. and R.M. Hirsch. 1992.
of the American Fisheries Society 114(1):92- Statistical methods in water resources.
96. Elsevier, Amsterdam, Netherlands.
Gray, J.S. 1989. Effects of Hillman, K., D.I. Walker, A.W.D.

environmental stress on species rich Larkum, and A.J. McComb. 1989.
assemblages. Biological Journal of the Productivity and nutrient limitation.
Linnean Society 37:19-32. Pages 635-685 in A.W.D. Larkum, A.J.

McComb, and S.A. Shepard (editors). in mesohaline Chesapeake Bay
Biology of Seagrasses. A treatise on the macrobenthos: spatial and temporal
biology of seagrasses with special reference patterns. Estuaries 10(3):227-245.
to the Australian region. Elsevier, New
York, NY. Honeyman, B.D. and P.H. Santschi.
1988. Metals in aquatic systems:
Hilsenhoff, W.L. 1987. An improved Predicting their scavenging residence
biotic index of organic stream pollution. times from laboratory data remains a
Great Lakes Entomologist 20:31-39. challenge. Environmental Science and
Technology 22:862-871.
Hinga, K.R. 1988. Seasonal predictions
for pollutant scavenging in two coastal Houde, E.D, and Zastrow, C.E. 1991.
environments using a model calibration Bay Anchovy Anchoa mitchilli. Pages 81-
based upon thorium scavenging. Marine 86 in S.L. Funderbunk, J.A. Mihursky,
Environmental Research 26:97-112. S.J. Jordan, and D. Riley (editors).
Habitat requirements for Chesapeake Bay
Holland, A.F. (editor). 1990. Near coastal living resources. Prepared for the Living
program plan for 1990: Estuaries. Resources Subcommittee, Chesapeake
EPA/600/4-90/033. Office of Research Bay Program.
and Development, USEPA,
Narragansett, RI. Howard, R.K., G.J. Edgar, and P.A.
Hutchings. 1989. Faunal assemblages of
Holland, A.F. 1985. Long-term seagrass beds. Pages 536-564 in A.W.D.
variation of macrobenthos in a Larkum, A.J. McComb, and S.A.
mesohaline region of the Chesapeake Shepard (editors). Biology of seagrasses.
Bay. Estuaries 8(2a):93-113. A treatise on the biology of seagrasses with
special reference to the Australian region.
Holland, A.F., A.T. Shaughnessy, L.C. Elsevier, New York, NY.
Scott, V.A. Dickens, J. Gerritsen, and J.A.
Ranasinghe. 1989. Long-term benthic Hughes, R.M. and D.P. Larsen. 1988.
monitoring and assessment program for the Ecoregions: An approach to surface
Maryland portion of the Chesapeake Bay: water protection. Journal of the Water
Interpretive report. CBRM-LTB/EST-2. Pollution Control Federation 60:486-493.
Prepared for MDNR, Power Plant
Research Program, Annapolis, Maryland Hughes, R.M., P.R. Kaufmann, A.T.
by Versar, Inc., Columbia, MD. Herlihy, T.M. Kincaid, L. Reynolds and
D.P. Larsen. 1998. A process for
Holland, A.F., A.T. Shaughnessy, L.C. developing and evaluating indices of
Scott, V.A. Dickens, J.A. Ranasinghe, fish assemblage integrity. Canadian
and J.K. Summers. 1988. Progress report: Journal of Fisheries and Aquatic Science
Long-term benthic monitoring and 55:1618-1631.
assessment program of the Maryland
portion of Chesapeake Bay (July 1986 - Hughes, R.M., D.P. Larsen, and J.M.
October 1987). PPRP-LTB/EST-88-1. Omernik. 1986. Regional reference
Prepared for MDNR, Power Plant sites: A method for assessing stream
Research Program, Annapolis, Maryland potentials. Environmental Management
by Versar, Inc., Columbia, MD. 10:629-635.
Holland, A.F., A.T. Shaughnessy, and Hurlbert, S.H. 1984. Pseudoreplication

M.H. Hiegel. 1987. Long-term variation and the design of ecological field
experiments. Ecological Monographs Kajak, Z. 1963. Analysis of quantitative
54(2). benthic methods. Ekologia Polska (A)
11:1-56.
Hutchinson, G.E. 1967. A treatise on
limnology. Wiley, New York, NY. Karr, J.R. 1991. Biological integrity: A
long-neglected aspect of water resource
Hyland, J.L., L. Balthis, C.T. Hackney, G. management. Ecological Applications
McRae, A.H. Ringwood, T.R. Snoots, 1:66-84.
R.F. Van Dolah, and T.L. Wade. 1998.
Environmental quality of estuaries of the Karr, J.R. 1981. Assessment of biotic
Carolinian Province: 1995. NOAA integrity using fish communities.
Technical Memorandum NOS ORCA Fisheries 6(6):21-27.
123. National Oceanic and Atmospheric
Administration, Charleston, SC. Karr, J.R., K.D. Fausch, P.L. Angermeier,
P.R. Yant, and I.J. Schlosser. 1986.
Hyland, J.L., T.J. Herrlinger, T.R. Snoots, Assessing biological integrity in running
A.H. Ringwood, R.F. Van Dolah, C.T. waters: A method and its rationale. Illinois
Hackney, G.A. Nelson, J.S. Rosen, and Natural History Survey, Spec. Publ. 5.
S.A. Kokkinakis. 1996. Environmental
quality of estuaries of the Carolinian Kemble, N., W. Brumbaugh, E. Brenson,
Province: 1994. Annual Statistical F. Dwyer, C. Ingersoll, D. Monda, and
Summary for the 1994 EMAP-Estuaries D. Woodward. 1994. Toxicity of metal
Demonstration Project in the Carolinian contaminated sediments from the Upper
Province. NOAA Technical Clark Fork River Montana to aquatic
Memorandum NOS ORCA 97. National invertebrates in laboratory exposures.
Oceanic and Atmospheric Environmental Toxicology and Chemistry
Administration/NOS, Office of Ocean 13:1985-1997.
Resources Conservation and
Assessment, Silver Spring, MD. 102 p. Kendall, D.K. 1983. The role of physical-
chemical factors in structuring subtidal
Ingersoll, C.G., P.S. Haverland, E.L. marine and estuarine benthos. Tech. Rep.
Brunson, T.J. Canfield, F.J. Dwyer, C.E. EL-83-2. U.S. Army Waterways Exp.
Henke, N.E. Kemble. 1996. Calculation Stn., Vicksburg, MS.
and evaluation of sediment effect
concentrations for the amphipod Klemm, D.J., G.J. Strober, and J.M.
Hyalella azteca and the midge Chironomus Lazorchak. 1992. Fish field and laboratory
riparius. Journal of Great Lakes Research methods for evaluating the biological
22(3): 602-623. integrity of surface waters. EPA/600/R-
92-111. USEPA, Cincinnati, OH.
Jordan, S., J. Carmichael, and B.
Richardson. 1992. Habitat measurements Komar, P.D. 1976. Beach processes and
and index of biotic integrity based on fish sedimentation. Prentice-Hall, Inc.
sampling in northern Chesapeake Bay. A Englewood Cliffs, NJ. 429 pp.
Proceedings: Estuarine and Near
Coastal Bioassessment and Biocriteria Krom, M.D. and R.A Berner. 1983.
Workshop, Annapolis, Maryland. Journal of Sedimentary Petrology 53, 660.
USEPA, Office of Science and
Technology, Washington, DC. Krumgalz, B.S. 1993. “Fingerprints”
approach to the identification of
anthropogenic trace metal sources in the

nearshore and estuarine environments. Environmental Toxicology and Chemistry
Estuaries 16(3A):488-495. 17(4):714-727.
LaPointe, B.E. and M.W. Clark. 1992. Long, E.R., D. D. MacDonald, J.C.
Nutrient inputs from the watershed and Cubbage, and C.G. Ingersoll. 1998b.
coastal eutrophication in the Florida Predicting the toxicity of sediment-
keys. Estuaries 15(4):465-476. associated trace metals with SEM:AVS
concentrations and dry weight-
Latimer, J., W. Boothman, R. Tobin, D. normalized concentrations: A critical
Keith, J. Kiddon, D. Scott, S. Jayaraman, comparison. Environmental Toxicology
R. McKinney, and G. Chmura. 1997. and Chemistry 17(4):972-974.
Historical reconstruction of contaminant
levels and ecological effects in a highly Long, E.R., A. Robertson, D.A. Wolfe,
contaminated estuary. 14th International J.Hameedi, and G.M. Sloane. 1996.
Conference of the Estuarine Research Estimates of the spatial extent of
Federation. Providence, RI. sediment toxicity in major U.S. estuaries.
Environmental Science & Technology
Lenat, D.R. 1993. A biotic index for the 30(12):3585-3592.
southeastern United States: Derivation
and list of tolerance values, with criteria Long, E.R., D.D. MacDonald, S.L. Smith,
for assigning water quality ratings. F.D. Calder. 1995. Incidence of adverse
Journal of the North American biological effects within ranges of
Benthological Society 12(3):279-290. chemical concentrations in marine and
estuarine sediments. Environmental
Lie, U. 1974. Distribution and structure Management 19:81-97.
of benthic assemblages in Puget Sound,
Washington, USA. Marine Biology Long, E.R. and L.G. Morgan. 1990. The
26:203-223. potential for biological effects of sediment-
sorbed contaminants tested in the National
Llansó, R.J. 1999. The distribution and Status and Trends Program. NOAA
structure of soft-bottom macrobenthos Technical Memorandum NOSOMA52.
in Puget Sound in relation to natural U.S. Department of Commerce, National
and anthropogenic factors. Puget Sound Oceanic and Atmospheric
Research 1998. Puget Sound Ambient Administration, National Ocean Service,
Monitoring Program, Olympia, WA: Rockville, MD.
760-771.
Long, E., M. Buchman, S. Bay, R.
Long, E.R. 1989. The use of the Breteler, R. Carr, P. Chapman, J. Hose,
sediment quality triad in classification of A. Lissner, J. Scott, and D. Wolfe. 1990.
sediment contamination. Marine Board, Comparative evaluation of five toxicity
National Research Council tests with sediments from San Francisco
Symposium/Workshop on Contaminated Bay and Tomales Bay, CA.
Marine Sediments. National Research Environmental Toxicology and Chemistry
Council, Washington, D.C. 9:1193-1214.
Long, E.R., L.J. Field, and D.D. Long, E.R. and P.M. Chapman. 1985. A
MacDonald. 1998a. Predicting toxicity sediment quality triad: Measures of
in marine sediments with numerical sediment contamination, toxicity and
sediment quality guidelines. infaunal community composition in
Puget Sound. Marine Pollution Bulletin National Research Council (NRC). 1989.
16:405-415. Contaminated Marine Sediments—
Assessment and Remediation. National
Luckenback, M.W., R.J. Diaz, and L.C. Academy Press, Washington, DC.
Schaffner. 1988. Benthic assessment
procedures. Nelson, W.G. 1990. Prospects for
development of an index of biotic
Ludwig, J.A. and J.F. Reynolds. 1988. integrity for evaluating habitat
Statistical ecology. A primer on methods degradation in coastal systems.
and computing. 337 p. John Wiley and Chemistry and Ecology 23: 152-165.
Sons, New York, NY.
Nelson, W.G., and F.D. Spoon. 1994a.
Mallin, M.A. 1994. Phytoplankton
Field verification of marine metrics
ecology of North Carolina estuaries.
developed for benthic habitats. Florida
Estuaries 17(3):561-574.
Institute of Technology, Oceanography
Program, Division of Marine and
Malone, T.C., D.J. Conley, T.R. Fisher,
Environmental Systems. Final Report to
P.M. Gilbert, L.W. Harding, and K.G.
Tetra Tech, Inc., Owings Mills, MD.
Sellner. 1996. Scales of nutrient-limited
phytoplankton productivity in
Nelson, W.G., and F.D. Spoon. 1994b.
Chesapeake Bay. Estuaries 19(2B):371-
Field Verification of the Use of Amphipods
385.
As Bioindicators in Marine Coastal
Ecosystems. Florida Institute of
Maryland Chamber of Commerce,
Technology, Oceanography Program,
personal communication, 1990.
Division of Marine and Environmental
Systems. Final Report to Tetra Tech,
MacDonald, D.D., R.S. Carr, F.D. Calder,
Inc., Owings Mills, MD.
E.R. Long, and C.G. Ingersoll. 1996.
Development and evaluation of
Nelson, W.G., R.J. Diaz, and F.D. Spoon.
sediment quality guidelines for Florida
1993. Comparison of results of marine
coastal waters. Ecotoxicology 5:253-278.
benthic metric development between
Chesapeake Bay and the Indian River
Mearns, A.J. and J.Q. Word. 1982.
Lagoon, Florida. Florida Institute of
Forecasting effects of sewage solids on
Technology, Division of Marine and
marine benthic communities. In G. F.
Environmental Systems, Final Report to
Mayer (editor). Ecological stress and the
Tetra Tech, Inc., Owings Mills, MD.
New York Bight: Science and management.
Estuarine Research Federation. 713 pp.
Nelson, M., P. Landrum, G. Burton, Jr., J.
Klaine, E. Crecelius, T. Byl, D. Gossiaux,
Miller, D.L., P.M. Leonard, R.M.
V. Tsymbal, L. Cleveland, C. Ingersoll,
Hughes, J.R. Karr, P.B. Moyle, L.H.
and G. Sasson-Brickson. 1993. Toxicity
Schrader, B.A. Thompson, R.A. Daniels,
of contaminated sediments in dilution
K.D. Fausch, G.A. Fitzhugh, J.R.
series with control sediments.
Gammon, D.B. Halliwell, P.L.
Chemosphere 27:1789-1812.
Angermeier, and D.J. Orth. 1988.
Regional applications of an index of
Nixon, S.W., C.D. Hunt and B.L.
biotic integrity for use in water resource
Nowicki. 1986. The retention of
management. Fisheries 13:12-20.
nutrients (C, N, P), heavy metals (Mn,
Cd, Pb, Cu), and petroleum
hydrocarbons in Narragansett Bay.

Pages 99-122 in P. Lasserre and J.M. the Association of American Geographers
Martin (editors). Biogeochemical Processes 77(1):118-125.
at the Land-Sea Boundary. Elsevier, New
York, NY. Oreskes, N., K. Schrader-Frechette, and
K. Belitz. 1994. Verification, validation,
O’Connor, T.P, A.Y. Cantillo, and G.G. and confirmation of numerical models
Lauenstein. 1994. Monitoring of in the earth sciences. Science 263:641-
temporal trends in chemical 646.
contamination by the NOAA National
Status and Trends Mussel Watch Project. Orth, R.J., J.F. Nowak, G.F. Anderson,
Pages 29-50 in K.J.M. Kramer (editor). and J.R. Whiting. 1993. Distribution of
Biomonitoring of Coastal Waters and submerged aquatic vegetation in the
Estuaries. CRC Press, Inc., Boca Raton, Chesapeake Bay and its tributaries and
FL. Chincoteague Bay - 1992. Prepared by
Virginia Institute of Marine Science,
Odum, E.P. 1971. Fundamentals of Gloucester Point, VA for the USEPA,
ecology, 3rd Edition. W.B. Saunders Co. Chesapeake Bay Program Office,
Philadelphia, PA. Annapolis, MD.
Odum, W. E. 1970. Insidious alteration Overton, W.S., D. White, and D.L.

of the estuarine environment. Stevens. 1990. Design report for EMAP:
Transactions of the American Fisheries Environmental Monitoring Assessment
Society 4:836-850. Program. EPA/600/3-91/053. U.S.
Environmental Protection Agency,
Odum, W.E. and C.C. McIvor. 1990. Office of Research and Development,
Mangroves. Chapter 15 in Myers, R.L. Washington, DC.
and J.J. Ewel (editors). Ecosystems of
Florida. University of Central Florida Pait, A.S., D.R.G. Farrow, J.A. Lowe, and
Press. P.A. Pacheis. 1989. Agricultural pesticide
use in estuarine drainage areas: A
Office of Technology Assessment (OTA). preliminary summary for selected pesticides.
1987. Wastes in marine environments. Strategic Assessment Branch Office of
OTA, Washington, DC. Oceanography and Marine Assessment,
NOAA, Rockville, MD.
Ohio EPA. 1990. The use of biocriteria in
the Ohio EPA surface water monitoring and Patterson, R.T. 1990. Intertidal benthic
assessment program. Ecological foraminiferal biofaces on the Fraser river
Assessment Section, Division of Water delta - British Columbia - Modern
Quality Planning and Assessments, distribution and paleoecological
Ohio EPA, Columbus, OH. August 22. importance. Micropaleontology 36:229-
245.
Ohio EPA. 1987. Biological criteria for the
protection of aquatic life. Vols. 1-3. Paul, J.F., J.H. Gentile, K.J. Scott, S.C.
Monitor. Assess. Prog., Surface Water Schimmel, D.E. Campbell, and R.W.
Sec., Div. Water Quality, Ohio EPA, Latimer. 1999. EMAP-Virginian Province
Columbus, OH. Four-Year Assessment Report (1990-1993).
EPA 600/R-99/004. U.S. Environmental
Omernik, J.M. 1987. Ecoregions of the Protection Agency, Atlantic Ecology
conterminous United States. Annals of Division, Narragansett, RI.
Paulsen, S.B., D.P. Larsen, P.R. Protection Agency/Corps of Engineers
Kaufmann, T.R. Whittier, J.R. Baker, Technical Committee on Criteria for
D.V. Peck, J. McGue, R.M. Hughes, D. Dredge and Fill Material.
McMullen, D.L. Stevens, J.L. Stoddard, J. Environmental Laboratory, U.S. Army
Lazorchak, W. Kinney, A.R. Selle, and R. Waterways Experiment Station,
Hjort. 1991. The Environmental Vicksburg, MS.
Monitoring and Assessment Program
(EMAP) - Surface waters monitoring Pond, S. and G.L. Pickard. 1983.
research plan, fiscal year 1991. Introductory dynamic oceanography. 3rd
EPA/600/3-91/022. USEPA, Corvallis, Edition. Pergamon Press, Inc., New
OR. York, NY.
Pearson, T.H. and R. Rosenberg. 1978. Puget Sound Estuary Program (PSEP).
Macrobenthic succession in relation to 1995. Recommended guidelines for
organic enrichment and pollution of the conducting laboratory bioassays on Puget
marine environment. Oceanography and Sound sediments. Prepared for USEPA
Marine Biology Annual Review 16:229-311. Region 10, Office of Puget-Sound,
Seattle, WA and Puget Sound Water
Peterman, R.M. 1990. The importance Quality Authority, Olympia, WA.
of reporting statistical power: The forest
decline and acidic deposition example. Puget Sound Water Quality Authority
Ecology 71(5):2024-2027. (PSWQA). 1991. Puget Sound update.
Second annual report of the Puget
Peters, J.A. 1988. Quality control Sound Ambient Monitoring Program.
infusion into stationary source PSWQA, Seattle, WA. 99 pp.
sampling. In L.H. Keith (editor).
Principles of environmental sampling. Puget Sound Water Quality Authority
American Chemical Society, (PSWQA). 1990. Puget Sound update.
Washington, DC. First annual report of the Puget Sound
Ambient Monitoring Program. PSWQA,
Peters, R.H. 1991. A critique for ecology. Seattle, WA. 89 pp.
Cambridge University Press,
Cambridge, MA. Puget Sound Water Quality Authority
(PSWQA). 1988. Puget Sound ambient
Pielou, E.C. 1977. Mathematical ecology. monitoring program, monitoring
John Wiley & Sons, Inc., New York, NY. management committee. Final Report.
385 pp. PSWQA, Seattle, WA. 145 pp.
Plafkin, J.L., M.T. Barbour, K.D. Porter, Rabalais, N.N. 1990. Biological
S.K. Gross, and R.M. Hughes. 1989. communities of the south Texas
Rapid bioassessment protocols for use in continental shelf. American Zoologist
streams and rivers: Benthic 30:77-87.
macroinvertebrates and fish. EPA/440/4-
89-001. USEPA, Office of Water, Rabalais, N.N., M.J. Dagg, and D.F.
Washington, DC. Boesch. 1985. Nationwide review of
oxygen depletion and eutrophication in
Plumb, R.H. 1981. Procedure for handling estuarine and coastal waters: Gulf of
and chemical analysis of sediment and water Mexico (Alabama, Mississippi, Louisiana,
samples. Technical Report EPA/CE-81-1. and Texas). Final Report to U.S.
Prepared for the U.S. Environmental Department of Commerce, NOAA,

Ocean Assessment Division, Rockville, Reish, D. J. and J. L. Bernard. 1960.
MD. Field toxicity tests in marine water
utilizing the polychaetous annelid
Rakoncinski, C.F., S.S. Brown, G.R. Capitella capitata (Fabricius). Pacific
Gaston, R.W. Heard, W.W. Walker, and Naturalist 1:1-8.
J.K. Summers. 1997. Macrobenthic
responses to natural and contaminant- Reishi D. and J. Lemay. 1988. Bioassay
related gradients in northern Gulf of manual for dredged materials. US Army
Mexico estuaries. Ecological Applications Corps of Engineers, Los Angeles
7:1278-1298. District, Los Angeles, CA, Technical
Report DACW-09-83R-005.
Rakocinski, C., R.W. Heard, T. Simons,
and D. Gledhill. 1991. Reynoldson, T.B. and M.A. Zarull. 1993.
Macroinvertebrate associations from An approach to the development of
beaches of selected barrier islands in the biological sediment guidelines. Pages
Northern Gulf of Mexico: Important 177-200 in S. Woodley, J. Kay, and G.
environmental relationships. Bulletin of Grancis (editors). Ecological Integrity and
Marine Science 48:689-701. the Management of Ecosystems. St. Lucie
Press.
Ranasinghe, J.A., D.M. Dauer, L.C.
Schaffnter, R.J. Diaz. 1994. Chesapeake Rhoads, D.C. 1974. Organism-sediment
Bay Benthic Community Restoration Goals. relations on the muddy sea floor.
Chesapeake Bay Program Office, 68-D9- Oceanography and Marine Biology Annual
0166; Chesapeake Bay Research & Review 12:263-300.
Monitoring Division, CB92-006-004.
Sanford, L.P., K.G. Sellner, and D.L.
Ranasinghe, J.A., L.C. Scott, and R. Breitburg. 1990. Covariability of
Newport. 1992. Chesapeake Bay water dissolved oxygen with physical
quality monitoring program: long-term characteristics in the summertime
benthic monitoring and assessment Chesapeake Bay. Journal of Marine
component. Vol. I. Draft. Prepared by Research 48:567-590.
Versar, Inc., Columbia, Maryland, for
the Maryland Department of Santangelo, R. 1996. County Sanitation
Environment, Baltimore, MD. Districts of Orange County, 10844 Ellis
Ave., Fountain Valley, CA 92728.
Reckhow, K.H. and W. Warren-Hicks.
1996. Biological criteria: Technical Sarda, N. and G. Burton, Jr. 1995.
guidance for survey design and statistical Ammonia variation in sediments:
evaluation of biosurvey data. Prepared by spatial, temporal, and method-related
School of the Environment, Duke effects. Environmental Toxicology and
University, Durham, NC for USEPA, Chemistry 14:1499-1506.
Office of Science and Technology,
Health and Ecological Criteria Division, Schimmel, S.C., B.D. Melzian, D.E.
Washington, DC. Campbell, C.J. Stubel, S.J. Benyi, J.S.
Rosen, and H.W. Buffum. 1994.
Reid, G.K. and R.D. Wood. 1976. Statistical Summary: EMAP-Estuaries
Ecology of inland waters and estuaries. D. Virginian Province - 1991. EPA/620/R-
Van Nostrand Company, New York, 94/005. Office of Research and
NY. 485 pp. Development, USEPA, Narragansett, RI.
Schindler, D.W. 1988. Effects of acid 1984. The estuarine interaction of
rain on freshwater ecosystems. Science nutrients, organics, and metals: A case
239:149-158. study in the Delaware Estuary. Pages
241-258 in V.S. Kennedy (editor). The
Schindler, D.W. 1971. A hypothesis to estuary as a filter. Academic Press,
explain differences and similarities Orlando, FL.
among lakes in the Experimental Lakes
Area, northwestern Ontario. Journal of Shepard, S.A., A.J. McComb, D.A.
the Fisheries Research Board of Canada Bulthis, V. Neverauskas, D.A.
28:295-301. Steffensen, and R. West. 1989. Decline
of seagrasses. Pages 346-393 in A.W.D.
Schindler, D.W., S.E.M. Kasian and R.H. Larkum, A.J. McComb, and S.A.
Hesslein. 1989. Biological Shepard (editors). Biology of seagrasses.
impoverishment in lakes of the A treatise on the biology of seagrasses with
midwestern and northeastern United special reference to the Australian region.
States from acid rain. Environmental Elsevier, New York, NY.
Science and Technology 23:573-580.
Simenstad, C.A., C.D. Tanner, R.M.
Schlekat, C.E., B.L. McGee, D.M. Thom, and L.L. Conquest. 1991. Puget
Boward, E. Reinharz, D.J. Velinsky, and Sound Estuary Program: Estuarine habitat
T.L. Wade. 1994. Tidal river sediments assessment protocol. EPA 910/9-91-037.
in the Washington, DC area. III. Prepared for USEPA, Region 10, Office
Biological effects associated with of Puget Sound, Seattle, WA. 201 pp.
sediment contamination. Estuaries
17(2):334-344. Simpson, B.L., R. Aaron, J. Betz, D.
Hicks, J. van der Kreeke, and B. Yokel.
Schroeder, W.W. 1979. The dissolved 1979. The Naples Bay Study. Prepared
oxygen puzzle of the Mobile estuary. In for the Collier County Conservancy,
Jr. and J.P. Smith (editors). H.A. Naples, FL.
Loyacano, Symposium on the Natural
Resources of the Mobile Estuary, Alabama, Smith, S.M. and G.L. Hitchcock. 1994.
May 1979. Alabama Coastal Area Board, Nutrient enrichments and
Mississippi-Alabama Sea Grant phytoplankton growth in the surface
Consortium, U.S. Fish and Wildlife waters of the Louisiana Bight. Estuaries
Service. 17(4):740-753.
Schubel, J.R. and H.H. Carter. 1984. The Smith, R.W., M. Bergen, S.B. Weisberg,
estuary as a filter for fine-grained D. Cadien, A. Dalkey, D. Montagne, J.K.
suspended sediment. Pages 81-104 in Stull, & R.G. Velarde. 2000. Benthic
V.S. Kennedy (editor). The Estuary as a response index for assessing infaunal
Filter. Academic Press, Orlando, FL. communities on the mainland shelf of
southern California. Ecological
Sen Gupta, B.K., R.E. Turner and N.N. Applications. In press.
Rabalais. 1996. Seasonal oxygen
depletion in continental-shelf waters of Snedecor, G.W. and W.G. Cochran.
Louisiana: Historical record of benthic 1980. Statistical methods. 7th edition. The
foraminifers. Geology 24(3):227-230. Iowa State University Press, Ames, IA.
Sharpe, J.H., J.R. Pennock, T.M. Church, Snelgrove, P.V.R. and C.A. Butman.
T.M. Tramontano, and L.A. Cifuentes. 1994. Animal-sediment relationships

revisited: Cause versus effect. Environmental Protection Agency,
Oceanography and Marine Biology Annual Office of Research and Development,
Review 32:111-177. Environmental Research Laboratory.
EPA/620/R-94/
Southerland, M.T. and J.B. Stribling.
1995. Status of biological criteria Summers, J.K., T.L. Wade, V.D. Engle,
development and implementation. and Z.A. Malneb. 1996. Normalization
Pages 81-96 in W.S. Davis and T.P. of metal concentrations in estuarine
Simon (editors). Biological assessment and sediments from the Gulf of Mexico.
criteria: Tools for water resources planning Estuaries 19(3):581-594.
and decision making. Lewis Publishers,
Boca Raton, FL. Summers, J.K., J.M. Macauley, P.T.
Heitmuller, V.D. Engle, A.M. Adams,
Stevenson, J.C., L.W. Staver, & K.W. and G.T. Brooks. 1993. Statistical
Staver. 1993. Water quality associated summary: EMAP-Estuaries Louisianian
with survival of submersed aquatic Province - 1991. EPA/600/R-93/001.
vegetation along an estuarine gradient. USEPA, Office of Research and
Estuaries 16(2)346-360. Development, Gulf Breeze, FL.
Stickney, R.R. 1984. Estuarine ecology of Summers, J.K. and V.D. Engle. 1993.
the southeastern United States and Gulf of Evaluation of sampling strategies to
Mexico. Texas A & M University Press, characterize dissolved oxygen
College Station, TX. conditions in northern Gulf of Mexico
estuaries. Environmental Monitoring and
Stoermer, E.F., J.A. Wolin, C.L. Schelske, Assessment 24:219-229.
and D.J. Conley. 1990. Siliceous
microfossil succession in Lake Michigan. Summers, J.K., J.M. Macauley, and P.T.
Limnology and Oceanography 35:959-967. Heitmuller. 1992. Field activities report:
Louisianian Province USEPA, Office of
Strobel, C.J., H.W. Buffum, S.J. Benyi, Research and Development,
E.A. Petrocelli, D.R. Reifsteck, and D.J. Environmental Research Laboratory,
Keith. 1995. Statistical Summary: EMAP- Gulf Breeze, FL. ERL-Gulf Breeze
Estuaries Virginian Province - 1990 to Contribution No. SR-118.
1993. EPA/620/R-94/026. U.S.
Environmental Protection Agency, Suter, G.W., II. 1993. Ecological risk
National Health and Environmental assessment. Lewis Publishers, Boca
Effects Research Laboratory, Atlantic Raton, FL.
Ecology Division, Narragansett, RI.
Swartz, R., D. Schults, R. Ozretich, J.
Strobel, C.J., S.J. Benyi, D.J. Keith, H.W. Lamberson, F. Cole, T. DeWitt. 1995.
Buffum, and E.A. Petrocelli. 1994. PAH: A model to predict the toxicity of
Statistical summary: EMAP-Estuaries polynuclear aromatic hydrocarbon
Virginian Province - 1992. EPA/620/R- mixtures in field collected sediments.
94/019. USEPA, Environmental Environmental Toxicology and Chemistry
Research Laboratory, Narragansett, RI. 14:1972-1987.
Summers J.K. 1994. (EMAP-Estuaries - A Swartz, R.C., F.A. Cole, J.O. Lamberson,
report on the condition of the estuaries of the S.P. Ferraro, D.W. Schults, W.A. DeBen,
United States in 1990-1993: A program in H. Lee II, and R.J. Ozretich. 1994.
progress.) Gulf Breeze (FL): U.S. Sediment toxicity, contaminations and
amphipod abundance at a DDT-and Thompson, S.K. 1992. Sampling. John
dieldrin-contaminated site in San Wiley & Sons, Inc., New York, NY. 343
Francisco Bay. Environmental Toxicology pp.
and Chemistry 13(6):949-962.
Turekian, K.K. 1977. The fate of metals
Swartz, R.C., F.A. Cole, D.W. Schults, in the oceans. Geochimica et
and W.A. DeBen. 1986. Ecological Cosmochimica Acta 41:1139-1144.
changes in the Southern California Bight
near a large sewage outfall: Benthic Turner, R.E. and N.N. Rabalais. 1994.
conditions in 1980 and 1983. Marine Coastal eutrophication near the
Ecology Progress Series 31:1-13. Mississippi River delta. Nature 368:619-
621.
Swartz, R.C., D.W. Schults, G.R.
Ditsworth, W.A. DeBen, and F.A. Cole. Turner, R.E., W.W. Schroder, and W.J.
1985. Sediment toxicity, contamination, Wiseman. 1987. The role of
and macrobenthic communities near a stratification in the deoxygenation of
large sewage outfall. Pages 152-175 in Mobile Bay and adjacent shelf bottom
T.P. Boyle (editor). Validation and waters. Estuaries 10:13-19.
predictability of laboratory methods for
assessing the fate and effects of U.S. Army Corps of Engineers. 1996. A
contaminants in aquatic ecosystems, ASTM comparison of the benthic macrofaunal
STP 865. American Society for Testing resources within the Bethany Beach Sand
and Materials, Philadelphia. Borrow Area. Prepared for U.S. Army
Corps of Engineers, Philadelphia
Symposium on the Classification of District by Versar, Inc., Columbia, MD.
Brackish Waters. 1958. The Venice
System for the Classification of Marine U.S. Environmental Protection Agency
Waters According to Salinity. Oikos (USEPA). 1998a. EPA requirements for
9:311-312. quality assurance project plans for
environmental data operations. EPA
ter Braak, C.J.F. 1986. Canonical QA/R-5. U.S. Environmental Protection
correspondence analysis: new Agency, Quality Assurance Division,
eigenvector technique for multivariate Washington, DC 20460.
direct gradient analysis. Ecology
67:1167-1179. U.S. Environmental Protection Agency
(USEPA). 1998b. Lake and reservoir
Thomann, R.V. and J.A. Mueller. 1987. bioassessment and biocriteria technical
Principles of surface water quality modeling guidance document. U.S. Environmental
and control. Harper and Row Publishers, Protection Agency, Office of Water,
New York, NY. 694 pp. Washington, D.C. EPA-841-B-98-007.
Thompson, B.A., and G.R. Fitzhugh. U.S. Environmental Protection Agency

1986. A use attainability study: An (USEPA). 1996a. Biological criteria:
evaluation of fish and macroinvertebrate Technical guidance for streams and small
assemblages of the Lower Calcasieu River, rivers. EPA 822-B-96-001. U.S.
Louisiana. LSU-CFI-85-29. Louisiana Environmental Protection Agency,
State University Center for Wetland Office of Water, Washington, DC.
Resources, Coastal Fisheries Institute,
Baton Rouge, LA. U.S. Environmental Protection Agency
(USEPA). 1996b. Recommended

guidelines for sampling and analyses in the activities, Rev. 200. U.S. Environmental
Chesapeake Bay monitoring program. Protection Agency, Las Vegas, NV. EPA
CBP/TRS 148/96. EPA 903-R-006. 600-X-91-080.
Chesapeake Bay Program, Annapolis,
MD. U.S. Environmental Protection Agency
(USEPA). 1993a. Environmental
U.S. Environmental Protection Agency Monitoring and Assessment Program.
(USEPA). 1995. Bibliography of methods EMAP-Estuaries Louisianian Province.
for marine and estuarine monitoring. EPA 1993 Quality Assurance Project Plan.
842-B-95-002. USEPA, Office of Water, USEPA, Office of Research and
Office of Wetlands, Oceans, and Development, Washington, DC.
Watersheds, Oceans and Coastal
Protection Division, Washington, DC. U.S. Environmental Protection Agency
(USEPA). 1993b (draft final). EPA
U.S. Environmental Protection Agency requirements for quality assurance project
(USEPA). 1994a. CWA Section 403: plans for environmental data operations.
Procedural and monitoring guidance. EPA EPA QA/R-5. Quality Assurance
842-B-94-003. Office of Wetlands, Management Staff, USEPA, Washington,
Oceans, and Watersheds, Oceans and DC.
Coastal Protection Division, USEPA,
Washington, DC. U.S. Environmental Protection Agency
(USEPA). 1992. Monitoring guidance for
U.S. Environmental Protection Agency the national estuary program. Final. EPA
(USEPA). 1994b. Methods for measuring 842-B-92-004. Office of Water, Oceans,
the toxicity of sediment associated and Coastal Protection Division,
contaminants with estuarine and marine USEPA, Washington, DC.
amphipods. EPA-600/R-94/025,
Narragansett, RI. U.S. Environmental Protection Agency
(USEPA). 1990. Biological criteria:
U.S. Environmental Protection Agency National program guidance for surface
(USEPA). 1994c (draft). Generic quality waters. EPA-440/5-90-004. USEPA,
assurance project plan guidance for Office of Water, Office of Regulations
programs using community-level biological and Standards, Criteria and Standards
assessment in streams and rivers. Prepared Division, Washington, DC.
by Tetra Tech, Inc. for Assessment and
Watershed Protection, USEPA, U.S. Environmental Protection Agency
Washington, DC. August 1. (USEPA). 1987. Surface water
monitoring: A framework for change.
U.S. Environmental Protection Agency USEPA, Office of Water, Office of Policy,
(USEPA). 1994d. Guidance for the data Planning and Evaluation, Washington,
quality objectives process. EPA 600/R- DC.
96/055. U.S. Environmental Protection
Agency, Office of Research and U.S. Environmental Protection Agency
Development, Washington, DC. (USEPA). 1986-1991. Recommended
protocols for measuring selected
U.S. Environmental Protection Agency environmental variables in Puget Sound.
(USEPA). 1994e. Environmental Looseleaf. Region 10, Puget Sound
Monitoring and Assessment Program: Estuary Program, USEPA, Seattle, WA.
Integrated quality assurance project plan for
the Surface Waters Resource Group, 1994
Vernberg, F. S. 1972. Dissolved gases. Weaver, G. 1984. PCB contamination in
Pages 1491-1526 In O. Kinne (editor). and around New Bedford, MA.
Marine Ecology , New York, Wiley- Estuaries 18:22A-27A.
Interscience. Volume I, Part 3.
Weinstein, M.P., S.L. Weiss, and M.F.
Ward, T.J. 1989. The accumulation and Walters. 1980. Multiple determinants of
effects of metals in seagrass habitats. community structure in shallow marsh
Pages 797-820 In A.W.D. Larkum, A.J. habitats, Cape Fear River Estuary, North
McComb, and S.A. Shepard (editors). Carolina, USA. Marine Biology 48:227-
Biology of seagrasses. A treatise on the 243.
biology of seagrasses with special reference
to the Australian region. Elsevier, New Wiesberg, S.B., J.A. Ranasinghe, D.M.
York, NY. Dauer, L.C. Schaffner, R.J. Diaz, and J.B.
Frithsen. 1997. An estuarine benthic
Warwick, R.M. 1988. Analysis of Index of Biotic Integrity (B-IBI) for
community attributes of the Chesapeake Bay. Estuaries 20:149-158.
macrobenthos of Fierfjord/
Laugelundfjord at taxonomic levels Weisberg, S.B., J.B. Frithsen, A.F.
higher than species. Marine Ecology Holland, J.F. Paul, K.J. Scott, J.K.
Progress Series 46:167-170. Summers, H.T. Wilson, R. Valente, D.G.
Heimbuch, J. Gerritsen, S.C. Schimmel,
Warwick, R.M. and K.R. Clarke. 1991. and R.W. Latimer. 1993. EMAP-
A comparison of some methods for Estuaries Virginian Province 1990
analyzing changes in benthic Demonstration Project Report.
community structure. Journal of the EPA/620/R-93/006. Environmental
Marine Biological Association of the Research Laboratory, USEPA,
United Kingdom 71:225-244. Narragansett, RI.
Warwick, R.M., H.M. Platt, K.R. Clarke, Wilding, J.R. 1940. A new square-foot
J. Agard, and J. Gobin. 1990. Analysis aquatic sampler. Limnological Society of
of macroinvertebrate and macrobenthic America Special Publication, No. 4:1-4.
community structures in relation to
pollution and disturbance in Hamilton Wonnacott, T.H. and R.J. Wonnacott.
Harbor, Bermuda. Journal of 1969. Introductory Statistics. 2nd edition.
Experimental Marine Biology and Ecology John Wiley and Sons, Inc., New York,
138:119-142. NY.
Washington, H.G. 1984. Diversity, biotic Word, J. Q. 1980. The infaunal trophic
and similarity indices, a review with index. The 1980 Annual Report,
special relevance to aquatic ecosystems. Southern California Coastal Research
Water Research 18: 653-694. Project. Long Beach, CA. pp 19-39.
Watson, P.G. and T.E. Frickers. 1990. A Word, J.Q. 1978. The infaunal trophic
multilevel, in situ pore-water sampler index. 1978 Annual Report, Southern
for use in intertidal sediments and California Coastal Water Research
laboratory microcosms. Limnology and Project, Annual Report. Pages 19-39.
Oceanography 35:1381-1389.

Word, J.Q., T.J. Kauwling, and A.J.
Mearns. 1976. A comparative field study
of benthic sampling devices used in
Southern California benthic surveys.
Southern California Coastal Water
Research Project, 1500 East Imperial
Highway, El Segundo, CA.
Wright, J.F., D. Moss, P.D. Armitage,

and M.T. Furse. 1984. A preliminary
classification of running-water sites in
Great Britain based on
macroinvertebrate species and the
prediction of community type using
environmental data. Freshwater Biology
14:221-256.

EPA Estuarine Coastal Waters Tech Guidance 2000

Uploaded by

Copyright:

Available Formats

EPA Estuarine Coastal Waters Tech Guidance 2000

Uploaded by

Document Information

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

EPA Estuarine Coastal Waters Tech Guidance 2000

Uploaded by

Copyright:

Available Formats

United States Office of Water EPA-822-B-00-024

Environmental Protection 4304 December 2000

Estuarine and Coastal Marine

George R. Gibson, Jr., Project Leader (4304)

Michael L. Bowman Jeroen Gerritsen

George R. Gibson, Jr. (4304) Blaine D. Snyder

The suggested citation for this document is:

Estuarine and Coastal Marine Biocriteria Workgroup Attendees

Suzanne Bolton Cindy Driscoll

Michael L. Bowman Charles Eaton

Dan Campbell Larry Eaton

Jeroen Gerritsen Don Kelso

George Gibson, Jr. (4304) Steve Kent

Additional scientific, technical, editorial, and production contributions were made

CHAPTER 1: Introduction: Bioassessment and Biocriteria . . . . . . . . . . . . . . . . . . . . . . 1-1

CHAPTER 2: Biological Survey . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1

CHAPTER 3: Habitat Characterization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1

3.4 BOTTOM CHARACTERISTICS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-15

CHAPTER 4: Physical Classification and the Biological Reference Condition . . . . . . . 4-1

CHAPTER 5: Sampling Program Issues, Biological Assemblages, and Design . . . . . . 5-1

5.1.6 Epibenthos (Developmental) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-19

CHAPTER 6: Water Column & Bottom Characteristics . . . . . . . . . . . . . . . . . . . . . . . . . 6-1

CHAPTER 7: Tier 0: Desktop Screening . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1

7.6 BIOLOGICAL ASSEMBLAGES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2

CHAPTER 8: Tier 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-1

CHAPTER 9: Tier 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-1

CHAPTER 10: Tier 3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-1

10.1.1 Sampling Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-3

CHAPTER 11: Index Development . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11-1

CHAPTER 12: Quality Assurance: Design, Precision, and Management . . . . . . . . . . . 12-1

CHAPTER 13: Case Studies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-1

13.4.3 Study Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-25

1-2 Program interdependence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-10

1-3 The process for progressing from the classification of an estuary to

1-4 General comparison of Tiered Approach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-18

3-1 Chemicals measured in sediments by the EMAP-Estuaries program . . . . . . 3-19

4-1 Graphical representation of bioassessment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-3

4-2 Classification and assessment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-4

4-3 Biogeographical provinces. Adapted from Holland 1990 . . . . . . . . . . . . . . . . . 4-6

4-6 Estuarine and coastal marine biocriteria survey method useful

4-7 Hypothetical cumulative frequency distribution of metric values for all

5-1 Cross-section of sediment in clamshell bucket illustrating acceptable

5-2 Description of various sampling methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-28

11-1 The process for progressing from the classification of an estuary to

11-2 Mean number of species and salinity at EMAP-Estuaries sampling

11-3 Hypothetical box plot illustrating how a successful metric discriminates

11-5 Steps 1-3. Establishing site scores on a contamination gradient . . . . . . . . . 11-16

11-6 Step 5. Abundance of species A and contamination scores. . . . . . . . . . . . . . 11-17

12-1 Effect of increasing sample size from n1 to n2 on power . . . . . . . . . . . . . . . . . 12-4

12-2 Example sample size calculations for comparing proportions and

12-3 Six qualitative and quantitative data characteristics usually employed to

13-1 General location of the case studies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-2

13-3 Ponar samples: biotic index vs. salinity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-28

13-5 Development of biocriteria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-31

13-6 Bethany Beach - Ocean City study area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-40

13-7 Bethany Beach - Ocean City sampling locations . . . . . . . . . . . . . . . . . . . . . . . 13-41

13-8a Total number of macroinvertebrate individuals at Bethany Beach sites;

13-8b Total number of macroinvertebrate individuals at Ocean City sites;

13-9a Total number of macroinvertebrate taxa at Bethany Beach sites;

13-9b Total number of macroinvertebrate taxa at Ocean City sites; summer