Mercury (Hg) contamination is a global conservation threat to freshwater ecosystems, detected in even the protected lakes of Olympic National Park (Washington, USA). Although considered some of the most remote and pristine US ecosystems, these lakes are currently subject to multiple environmental stressors, including climate change and fish introductions; adding contaminants, such as Hg, could exacerbate the effects of these stressors on native species. Amphibians are undergoing large worldwide declines, which include declines in protected areas, such as our National Parks. Our goal is to better understand the effect of historically stocked fish in Olympic National Park on native amphibian Hg bioaccumulation. To minimize the need for lethal sampling of this already threatened group, we first examine how Hg concentrations in non-lethally sampled amphibian tissues correlated with whole-body Hg concentrations, depending on species and the different type of non-lethal tissue sample used. Second, we aimed to understand how a food web altered by fish impacted Hg bioaccumulation in native species. We measured Hg and stable isotopes of carbon and nitrogen in organisms across trophic levels from 18 subalpine lakes. We detected small shifts in salamander food web indices and minor changes to salamander Hg concentration associated with the presence of fish. Importantly, we found increased mercury trophic magnification slopes in lakes with fish compared to fishless lakes. This research provides evidence that historic fish introductions can elevate mercury exposure in pristine ecosystems compared to natural fishless lakes.