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Abstract Run-of-river power plants (ROR) represent the majority of hydroelectric plants worldwide. Their environmental impacts are not well documented and are believed to be limited, particularly regarding the contamination of food webs by methylmercury (MeHg), a neurotoxin. RORs are typically installed in small rivers where combined effects of watershed disturbances with dam construction can complicate environmental management. We report a multi-year case study on the Saint-Maurice River (Canada) where an unpredicted temporary increase in MeHg accumulation in predator fish was observed after the construction of two ROR plants. The associated pondages acted as sedimentation basins for mercury (Hg) and organic matter from a watershed disturbed by a forest fire and by logging. This fresh organic carbon likely fueled microbial MeHg production. Hg methylation was more associated with environmental conditions than to the presence of Hg, and main methylating microbial groups were identified. A constructed wetland was a site of significant Hg methylation but was not the main source of the fish Hg increase. Organic carbon degradation was the main driver of MeHg accumulation at the base of the food chain whereas trophic levels explained the variations at the top of the food chain. Overall, carbon cycling was a key driver of Hg dynamics in this system, and ROR plants can cause temporary (ca. 12 years) Hg increase in food webs when developed in disturbed watersheds, although this increase is smaller than for large reservoirs. Recommendations for future ROR construction are to establish a good environmental monitoring plan with initial high temporal resolution and to consider recent and potential watershed disturbances in the plan.