Aims We assessed the beta diversity of macroinvertebrates associated with aquatic macrophytes in a dam-regulated river floodplain. We tested two hypotheses: (1) macroinvertebrates associated with aquatic macrophytes have higher beta diversity (higher turnover and nestedness components) in the downstream areas closer to the São Francisco River compared to upstream sites; (2) closer lakes share a higher similarity of aquatic macroinvertebrates, disregarding their position relative to the dam. Methods We sampled four lakes, including two upstream (L1- natural and L2- regulated by a Small Hydropower Dam - SHD) and two downstream (L3, L4, unregulated) by the SHD. Results We corroborated our first hypothesis because we found a higher turnover of macroinvertebrates associated with aquatic macrophytes close to the São Francisco River (L4 downstream), where higher non-native mollusk species richness occurs, while we found higher nestedness upstream and downstream of the SHD (L1, L2, L3). We corroborated our second hypothesis, as closer lakes are more similar than distant lakes. Finally, these differences were consistent between lakes for emergent, floating leaf, and submerged aquatic macrophytes. Conclusions Aquatic macrophytes are essential habitats for macroinvertebrates in the Pandeiros River basin, with higher beta diversity in the lake closer to the São Francisco River.