Mercury (Hg) deposited onto the landscape can be transformed into methylmercury (MeHg), a neurotoxin that bioaccumulates up the aquatic food chain. Here, we report on Hg concentrations in snapping turtles (Chelydra serpentina) across New York State, USA. The objectives of this study were to: (1) test which landscape, water, and biometric characteristics correlate with total Hg (THg) concentrations in snapping turtles; and (2) determine whether soft tissue THg concentrations correlate with scute (shell) concentrations. Forty-eight turtles were sampled non-lethally from ten lakes and wetlands across New York to observe patterns under a range of ecosystem variables and water chemistry conditions. THg concentrations ranged from 0.041 to 1.50 μg/g and 0.47 to 7.43 μg/g wet weight of muscle tissue and shell, respectively. The vast majority of mercury (~94%) was in the MeHg form. Sixty-one percent of turtle muscle samples exceeded U.S. Environmental Protection Agency (U.S. EPA) consumption advisory limit of 0.3 μg Hg/g for fish. Muscle THg concentrations were significantly correlated with sulfate in water and the maximum elevation of the watershed. Shell THg concentrations were significantly correlated with the acid neutralizing capacity (ANC) of water, the maximum elevation of the watershed, the percent open water in the watershed, the lake to watershed size, and various forms of atmospheric Hg deposition. Thus, our results demonstrate that THg concentrations in snapping turtles are spatially variable, frequently exceed advisory limits, and are significantly correlated with several landscape and water characteristics.