Dams alter many aspects of riverine environments and can have broad effects on aquatic organisms and habitats both upstream and downstream. While dams and the associated reservoirs can provide many services to people (hydropower, recreation, flood control, navigation, etc.), they can negatively affect riverine ecosystems. In particular, hydropeaking dams affect downstream fish habitats by increasing variability in discharge and temperature. To assess the effects of Harris Dam on the Tallapoosa River, AL, operating under an adaptive management plan implemented in 2005, we sampled fish for community and diet analyses from four sites on the river: three in the regulated region downstream of the dam, and one unregulated site upstream. Fish were collected every other month using boat/barge electrofishing. We used Shannon’s H, nonmetric multidimensional scaling (NMDS), a multiresponse permutation procedure (MRPP), and indicator species analysis to quantify patterns in fish assemblage structure and determine how assemblages varied among sites. NMDS and MRPP indicated significant fish assemblage differences among sites with the tailrace fish assemblage being distinct from the other downstream sites, and sites becoming more similar to the upstream, unregulated site (relative to fish assemblages) with distance downstream of the tailrace. The tailrace fish assemblage included higher proportions of rheophilic species that may be better suited for variable and/or high flows. Altered fish assemblages demonstrated continued effects of Harris Dam on the downstream aquatic systems, particularly close to the dam. These effects may indicate further mitigation should be considered depending on conservation and management goals.