Resumo. Abstract Aim Floodplains are among the most biologically diverse systems in the world, where hydrological regime is recognized as crucial to structure aquatic communities. We predicted that i) structure of benthic metacommunity is nested in the drought and random in the flood season in a Neotropical floodplain. We expected to find ii) environmental homogenization during the flood season which may disrupt the nested pattern. Moreover, we identified habitats of high taxa richness of benthic invertebrates and characterized them by habitat type and fluvial systems. Methods We sampled benthic invertebrates from 36 habitats in the Upper Paraná River floodplain. We tested nestedness using NODF index and evaluated the environmental variability using the multivariate homogeneity of group dispersions (PERMDISP), separately for flood and drought periods. Results The environmental variability was lower during the flood. We found a nested distribution among benthic invertebrates in both flood and drought periods. The highest species richness values were recorded in small and unconnected lakes from Paraná fluvial system and some rivers and secondary channels, independent of the fluvial system. Chironomidae, Oligochaeta and Ostracoda were the most frequent taxa and were recorded in all habitats. Conclusion The nested distribution of benthic invertebrates is a consistent pattern for this metacommunity because its distribution was not disrupted by floods that homogenize limnological conditions and increase the connectivity among habitats. We also found that habitats with high taxa richness were both lotic and lentic in the three fluvial systems. Our findings emphasize that different habitats in different subsystems sustains the richness of the benthic invertebrates metacommunity in the Upper Paraná River floodplain over time.