The impacts of small impoundments on headwater streams have received little attention despite their potential to have local and broad-scale ecological impacts. These impoundments might alter stream hydrology, geomorphology, and facilitate the spread of invasive species. Given that prairie stream communities have adapted to highly variable conditions, they might resist disturbances associated with small impoundments. To test the resistance of aquatic communities to the disturbances associated with small impoundments, we surveyed intermittent headwater prairie streams in both unimpounded and impounded watersheds. We observed greater fish density and species richness in unimpounded watersheds and two species occupying a greater proportion of sites in unimpounded than impounded watersheds. In contrast to fish communities, we observed no difference in crayfish density or the community structure and biomass of aquatic insect and snail communities between unimpounded and impounded watersheds. Increased sensitivity to disturbances associated with small impoundments by fishes might be attributed to their limited dispersal capabilities.