Estuaries are among the most productive ecosystems on the planet and provide many important functions to the benefit of humans. Estuaries, however, are also under multiple anthropogenic threats, such as habitat degradation, pollution, eutrophication, and trophic downgrading through overharvesting of marine predators. These threats to estuaries come with a heavy cost through the loss of key ecosystem functions and services. The purpose of my dissertation was to characterize how anthropogenic threats affect estuarine communities in Elkhorn Slough, an estuary that provides habitat to a great diversity of organisms but is under threat through extreme nutrient loading and habitat modification.

In my first chapter I investigated how bottom-up (nutrients) and top-down (predation) forcing interact to influence seagrass beds. Using the recovery of sea otters (Enhydra lutris) I demonstrated that top predators can mediate the harmful effects of nutrient loading and eutrophication to eelgrass (Zostera marina) beds through the removal of crabs, which frees mesograzers to perform an important function: removing shade-causing algal epiphytes from seagrass leaves. I followed up on these results for my second chapter to develop a mechanistic understanding of eelgrass resilience in face of macroalgal blooms (Ulva spp.) that coincide with peak eelgrass production. Using a series of field experiments I demonstrated that sea otters can promote both eelgrass and Ulva at a seagrass-macroalgal ecotone, a process that benefits eelgrass resilience by enhancing Ulva's mesograzer assemblage that lowers the epiphyte load on eelgrass.

For my third and final chapter I used a 40 year data set of fish, water quality, and climate indices to determine the long-term effects of hypoxia on two important ecosystem services: the provision of biodiversity and nursery function. My results demonstrated that anthropogenic nutrient loading and subsequent hypoxia negatively impacted fish diversity and the nursery function for English sole (Parophrys vetulus). Despite ever increasing nutrient inputs, hypoxia was highly variable in time and space, and was mediated by climate, specifically El Niño events that increase flushing through increased precipitation as well as suppressing upwelling that brings hypoxic water from the deep sea. The suppression of hypoxia through El Niño events was a consistent pattern across estuaries in the northeast Pacific, providing important insight as to how climate change will affect anthropogenic threats to ecosystem services provided by estuaries.

My dissertation unravels some of the mysteries underlying ecosystem resilience in face of anthropogenic threats. Systems like Elkhorn Slough are critical for informing research and management as to how ecosystems function under intense stress. The rarity of available long-term data, along with the recovery of a foundation species - Zostera marina - and a model top predator - Enhydra lutris - made it possible to tease apart processes and mechanisms driving resilience over meaningful time scales. Furthermore, my dissertation highlights the importance of studying systems where resilience and recovery are occurring, as they will provide insight to inform management and policy in a world of increasing anthropogenic threats and changing climate.