Run‐of‐river dams produce lower greenhouse gas emissions than large hydropower projects, but there is a paucity of research on their potential ecotoxicological impacts through disruption of natural flow regimes. We used stable isotopes (δ13C, δ15N, δ34S) to reconstruct diet and trace methylmercury in a predatory river‐resident passerine, the American dipper (Cinclus mexicanus), at 7 regulated and 6 free‐flowing mountain streams in coastal British Columbia, Canada. Assimilated diets were comparable among regulated and unregulated streams, dominated by benthic macroinvertebrates and resident freshwater fish, with negligible contributions from anadromous Pacific salmon. Although invertebrates at unregulated streams were isotopically similar along their gradient, dippers and invertebrates sampled below dams on regulated streams had 34S‐depleted tissues, suggesting increased activity of sulfate‐reducing bacteria and more Hg methylation below the dams. Mercury concentrations in dipper blood (417.6 ± 74.1 standard error [SE] ng/g wet wt at regulated streams, 340.7 ± 42.7 SE ng/g wet wt at unregulated streams) and feathers (1564 .6 ± 367.2 SE ng/g dry wt regulated, 1149.0 ± 152.1 SE ng/g dry wt unregulated), however, were not significantly different between stream types. Relative to other passerines across western North America, dippers in these densely forested mountain streams experienced high mercury exposure; and one recently regulated stream supported dippers with mercury concentrations of potential toxicity concern (up to 8459.5 ng/g dry wt in feathers and 1824.6 ng/g wet wt in whole blood). Elevated mercury in dippers is likely attributable to the birds’ relatively high trophic position and high regional inorganic mercury deposition; however, biogeochemical conditions in reservoirs of some regulated streams may be contributing to methylmercury production.