The traditional Inuit diet includes wild birds, fish and marine mammals, which can contain high concentrations of the neurotoxicant methylmercury (MeHg). Hydroelectric development may increase MeHg concentrations in traditional foods. Consumption advisories are often used to mitigate such risks and can result in reduced intake of traditional foods. Data from a dietary survey, MeHg exposure assessment and risk analysis for individuals in three Inuit communities in Labrador, Canada (n = 1,145) in 2014 indicate reducing traditional food intake is likely to exacerbate deficiencies in n-3 polyunsaturated fatty acids and vitamins B12 and B2. Traditional foods accounted for < 5% of per-capita calories but up to 70% of nutrients consumed. Although consumption advisories could lower neurodevelopmental risks associated with an increase in MeHg exposure (90th-percentile ∆IQ = −0.12 vs. −0.34), they may lead to greater risks of cardiovascular mortality (90th-percentile increase: +58% to +116% vs. +25%) and cancer mortality (90th-percentile increase +2% to +4% vs. no increase). Conversely, greater consumption of locally caught salmon mostly unaffected by hydroelectric flooding would lower all these risks (90th-percentile ∆IQ = +0.4; cardiovascular risk: –45%; cancer risk: –1.4%). We thus conclude that continued consumption of traditional foods is essential for Inuit health in these communities.