Chemical contaminants are a threat to the Chesapeake Bay watershed, with mercury (Hg) among the most prevalent causes of impairment. Despite this, large-scale patterns of Hg concentrations, and the potential risks to fish, wildlife, and humans across the watershed, are poorly understood. We compiled fish Hg data from state monitoring programs and recent research efforts to address this knowledge gap and provide a comprehensive assessment of fish Hg concentrations in the watershed’s freshwater habitats. The resulting dataset consisted of nearly 8000 total Hg (THg) concentrations from 600 locations. Across the watershed, fish THg concentrations spanned a 44-fold range, with mean concentrations varying by 2.6- and 8.8-fold among major sub-watersheds and individual 8-digit hydrological units, respectively. Although, mean THg concentrations tended to be moderate, fish frequently exceeded benchmarks for potential adverse health effects, with 45, 48, and 36% of all samples exceeding benchmarks for human, avian piscivore, and fish risk, respectively. Importantly, the percentage of fish exceeding these benchmarks was not uniform among species or locations. The variation in fish THg concentrations among species and sites highlights the roles of waterbody, landscape, and ecological processes in shaping broad patterns in Hg risk across the watershed. We outline an integrated Hg monitoring program that could identify key factors influencing Hg concentrations across the watershed and facilitate the implementation of management strategies to mitigate the risks posed by Hg.