Anthropogenic activities resulting in elevated selenium (Se) levels in aquatic ecosystems can result in teratogenic and reproductive effects in fish and waterfowl. However, relationships between observed effects and exposure concentrations or body burdens are ambiguous. Therefore, it is critical to identify factors that affect Se ecotoxicity before defining adequate protective environmental regulations. One important political debate questions if Se ecotoxicity differs between standing (lentic) and flowing (lotic) waters and, if so, how this should be incorporated into the definition of protective criteria. In the present review, we compile and discuss the scarce literature regarding Se ecotoxicity in lotic systems, and we compare it to the substantial body of evidence for lentic systems. General differences between lentic and lotic systems with respect to ecology, hydrology, and biogeochemistry are identified and related to Se ecotoxicity. The limited knowledge regarding Se speciation in the biomagnification process is reviewed and put in context. Fundamental considerations suggest that Se ecotoxicity in lotic systems should be reduced compared to lentic systems, but we conclude that this statement is not substantiated by the existing data. Additionally, we identify critical gaps of knowledge that must be resolved in future studies before the argument can be decided conclusively.