Anthropogenic manipulation of aquatic habitats can profoundly alter mercury (Hg) cycling and bioaccumulation. The impoundment of fluvial systems is among the most common habitat manipulations and is known to increase fish Hg concentrations immediately following impoundment. However, it is not well understood how Hg concentrations differ between reservoirs and lakes at large spatial and temporal scales or how reservoir management influences fish Hg concentrations. This study evaluated total Hg (THg) concentrations in 64,386 fish from 883 reservoirs and 1387 lakes, across the western United States and Canada, to assess differences between reservoirs and lakes, as well as the influence of reservoir management on fish THg concentrations. Fish THg concentrations were 1.4-fold higher in reservoirs (0.13 ± 0.011 μg/g wet weight ± standard error) than lakes (0.09 ± 0.006), though this difference varied among ecoregions. Fish THg concentrations were 1.5- to 2.6-fold higher in reservoirs than lakes of the North American Deserts, Northern Forests, and Mediterranean California ecoregions, but did not differ between reservoirs and lakes in four other ecoregions. Fish THg concentrations peaked in three-year-old reservoirs then rapidly declined in 4–12 year old reservoirs. Water management was particularly important in influencing fish THg concentrations, which were up to 11-times higher in reservoirs with minimum water storage occurring in May, June, or July compared to reservoirs with minimum storage occurring in other months. Between-year changes in maximum water storage strongly influenced fish THg concentrations, but within-year fluctuations in water levels did not influence fish THg concentrations. Specifically, fish THg concentrations increased up to 3.2-fold over the range of between-year changes in maximum water storage in all ecoregions except Mediterranean California. These data highlight the role of reservoir creation and management in influencing fish THg concentrations and suggest that water management may provide an effective means of mitigating Hg bioaccumulation in some reservoirs.