We measured species richness, diversity, and abundance of fish in both shallow and deep water areas in regulated and unregulated sections of the Tallapoosa River in Alabama from July 1990 through September 1992 to compare the effects of flow regulation on fish assemblages in shallow and deep water habitats. Flow regulation had a greater effect on shallow water fish assemblages than on deep water fish assemblages. Species richness and diversity of shallow water fishes were reduced below two hydroelectric dams compared with unmodified river segments, and we attribute this to a reduction in species adapted to fluvial environments below the two dams. Additionally, the density of fish in shallow water areas of unregulated portions of the river was significantly (P<0.05) higher than the density at most of the regulated sites. No reductions in species richness or diversity below the two dams were observed for species inhabiting deep water areas. However, we collected a significantly (P<0.05) higher number of catostomid species in the unmodified river sections compared to the flow-regulated sections.