Unlike large dams which favor methylation of Hg in flooded soils over long periods, run-of-river dams are designed to flood a limited area of soils and are therefore not expected to significantly affect mercury (Hg) cycling or carbon processing. We studied the Hg and carbon cycles within food webs from several sectors along the Saint-Maurice River, Quebec, Canada, that differ in how they are influenced by two run-of-river dams and other watershed disturbances. We observed peak Hg concentrations in fish five-year postimpoundment, but these levels were reduced three years after this peak. Methylmercury concentrations in low trophic level fish and invertebrates were related to their carbon source (δ13C) rather than their trophic positions (δ15N). Biomagnification, measured by trophic magnification slopes, was driven mainly by methylmercury concentrations in low-trophic level organisms and environmental factors related to organic matter degradation and Hg-methylation. River sectors, δ13C and δ15N, predicted up to 80% of the variability in food web methylmercury concentrations. The installation of run-of-river dams and the related pondages, in association with other watershed disturbances, altered carbon processing, promoted Hg-methylation and its accumulation at the base of the food web, and led to a temporary increase in Hg levels in fish.