We studied spatiotemporal patterns of fish assemblage structure in the Neosho River, Kansas, a system impounded by low-head dams. Spatial variation in the fish assemblage was related to the location of dams that created alternating lotic and lentic stream reaches with differing fish assemblages. At upstream sites close to dams, assemblages were characterized by species associated with deeper, slower-flowing habitat. Assemblages at sites immediately downstream from dams had higher abundance of species common to shallow, swift-flowing habitat. Temporal variation in assemblage structure was stronger than spatial variation, and was associated with fish life history events such as spawning and recruitment, as well as seasonal changes in environmental conditions. Our results suggest that low-head dams can influence spatial patterns of fish assemblage structure in systems such as the Neosho River and that such assemblages also vary seasonally.