Artificial light at night is gaining attention for its potential to alter ecosystems. Although terrestrial ecologists have observed that artificial light at night may disrupt migrations, feeding, and other important ecological functions, we know comparatively little about the role artificial light might play in disrupting freshwater and riparian ecosystems. We identify and discuss four future research domains that artificial light may influence in freshwater and associated terrestrial ecosystems, with an emphasis on running waters: (1) dispersal, (2) population genetics and evolution, (3) ecosystem functioning, and (4) potential interactions with other stressors. We suggest that future experimental and modeling studies should focus on the effects of different spectral emissions by different light sources on freshwater organisms, the spatial and temporal scale over which artificial light acts, and the magnitude of change in light at night across the landscape relative to the distribution of running and standing waters. Improved knowledge about the effects of artificial light on freshwater ecosystems will inform policy decisions about changes to artificial light spectral emissions and distributions.