Estuaries are globally important areas for methylmercury bioaccumulation because of high methylmercury production rates and use by fish and wildlife. We measured total mercury (THg) concentrations in ten fish species from 32 wetland and open bay sites in San Francisco Bay Estuary (2005–2008). Fish THg concentrations (μg/g dry weight ± standard error) differed by up to 7.4× among estuary habitats. Concentrations were lowest in open bay (0.17 ± 0.02) and tidal wetlands (0.42 ± 0.02), and highest in managed seasonal saline wetlands (1.27 ± 0.05) and decommissioned high salinity salt ponds (1.14 ± 0.07). Mercury also differed among fishes, with Mississippi silversides (0.87 ± 0.03) having the highest and longjaw mudsuckers (0.37 ± 0.01) the lowest concentrations. Overall, 26% and 12% of fish exceeded toxicity benchmarks for fish (0.20 μg/g wet weight) and piscivorous bird (0.30 μg/g wet weight) health, respectively. Our results suggest that despite managed wetlands' limited abundance within estuaries, they may be disproportionately important habitats of Hg risk to coastal wildlife.