Developing Canadian hydroelectric resources is a key component of North American plans for meeting future energy demands. Microbial production of the bioaccumulative neurotoxin methylmercury (MeHg) is stimulated in newly flooded soils by degradation of labile organic carbon and associated changes in geochemical conditions. We find all 22 Canadian hydroelectric facilities being considered for near-term development are located within 100 km of indigenous communities. For a facility in Labrador, Canada (Muskrat Falls) with planned completion in 2017, we probabilistically modeled peak MeHg enrichment relative to measured baseline conditions in the river to be impounded, downstream estuary, locally harvested fish, birds and seals, and three Inuit communities. Results show a projected 10-fold increase in riverine MeHg levels and a 2.6-fold increase in estuarine surface waters. MeHg concentrations in locally caught species increase 1.3 to 10-fold depending on time spent foraging in different environments. Mean Inuit MeHg exposure is forecasted to double following flooding and over half of the women of childbearing age and young children in the most northern community are projected to exceed the U.S. EPA's reference dose. Equal or greater aqueous MeHg concentrations relative to Muskrat Falls are forecasted for 11 sites across Canada, suggesting the need for mitigation measures prior to flooding.