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Mountain lakes, while seemingly pristine, have been subjected to historical fish stocking practices and exposure to atmospherically deposited contaminants like mercury. Mercury bioaccumulation in these ecosystems varies widely due to strong environmental gradients, and there are complex, hierarchical factors that affect mercury transport and loading, methylmercury production, and food web biomagnification. We sought to assess how representative variables associated with watershed, lake, and food web‐scale processes—specifically, catchment tree cover, lake benthic primary production, and fish diet, respectively—are associated with mercury concentrations in mountain lake fish. Mean fish mercury concentrations varied threefold between lakes, with nearshore tree cover and fish diet accounting for the most variance in fish mercury. Tree cover was likely positively correlated to fish Hg due to its contributions to local deposition and its effect on lake biogeochemistry. Fish with benthic diets tended to have higher mercury concentrations, illustrating that food web processes are an important consideration when investigating drivers of contaminant bioaccumulation. Our results suggest that both landscape and ecological factors are determinants of fish mercury bioaccumulation, and thus variables at multiple scales should be considered when managing mountain lake food webs for mercury exposure risk.