Anthropogenic activities resulting in releases of selenium-laden waste streams threaten freshwater ecosystems. Lake ecosystems demand special consideration because they are characterized by prolonged retention of selenium and continuous cycling of the element through the food chain, through which it becomes available to toxicologically susceptible egg-laying vertebrates. This study documents the current selenium burden of lakes in North Carolina (NC) with historic selenium inputs from nearby coal-fired power plants. We measured selenium concentrations in surface waters, sediment pore waters, and resident fish species from coal combustion residual (CCR)-impacted lakes and paired reference lakes. The data are related to levels of recent selenium inputs and analyzed in the context of recently updated federal criteria for the protection of aquatic life. We show that the Se content of fish from lakes with the highest selenium inputs regularly exceed these criteria and are comparable to those measured during historic fish extirpation events in the United States. Large legacy depositions of CCRs within reservoir sediments are likely to sustain Se toxicity for many years despite recent laws to limit CCR discharge into surface waters in NC. Importantly, the widespread use of high-selenium coals for electricity generation extends the potential risk for aquatic ecosystem impacts beyond U.S. borders.