Private wells are a critical drinking water source and are susceptible to contamination from flooding. Opportunistic pathogens (OPs), such as Legionella, are an increasing source of drinking water-related outbreaks, but are poorly characterized in private wells. Here we conducted a molecular survey of OPs in private wells and plumbing systems shortly after the 2016 Louisiana flood. Detection frequency of fecal indicators was not notably high (total coliform 24.8% and Escherichia coli 3.5% in 113 private wells) ten weeks after flooding. Gene markers of Legionella spp., L. pneumophila, and Naegleria fowleri were detected in 77.5%, 15.0%, and 20.0% of a subset of 40 homes that were tested specifically for these OPs, respectively. Legionella spp. varied from 8.4 gc mL⁻¹ to 1.8 × 10⁴ gc mL⁻¹ in first draw and flushed water. Positive detections and levels of Legionella spp., as well as positive detections of L. pneumophila, were correlated with total bacterial numbers (measured as 16S rRNA gene copy numbers), suggesting that total bacterial numbers could be an indicator of OP occurrence under the conditions of private wells, which usually do not have disinfection treatment installed. Further, Legionella spp. positivity in first draw water from cold and hot taps was associated with their detection in flushed water, suggesting that the well itself can be a source of OPs. OP detection was not predictable from total coliform, well characteristics, or observable well damage, but was associated with higher metals in flushed water resulting from plumbing corrosion. Given that the majority of Legionnaires' disease cases are sporadic, private wells merit greater attention as a potential source of exposure.