River corridors are interspersed with a mosaic of habitats that promotes biodiversity. Flow is important in shaping physical habitats, driving abiotic processes and maintaining biotic communities, but climate change and the associated hydrological drying threaten these systems. This study aimed to understand role of lateral river corridor habitats and hydrological drying in structuring the diversity of macroinvertebrates. Aquatic invertebrate assemblages were sampled during a descending limb of the hydrograph at six sites on of the Savannah River, southeastern, USA. Floodplain, oxbow lake and the river channel habitats were sampled within six sites for a total of 113 samples. We found differences among alpha diversity of macroinvertebrates, including Shannon, inverse Simpson and rarefied richness between habitats using linear mixed model. Oxbow lakes had the highest alpha diversity, with the highest number of genera. We also found differences in beta diversity, where Bray-Curtis dissimilarity accounted for 43% of the variation in community composition, where habitats were the dominant driver of variation (26.5%) and drought stage accounted for a smaller portion (4.8%) of variation. However, a significant interaction revealed that drought did not shift communities in a similar patterns among habitats and multivariate dispersion showed that mid-drought had a higher dispersion than early or late. Understanding the influence drought will have on aquatic invertebrates in these ecosystems will be critical to anticipate changes and develop strategies to protect freshwater ecosystems. The loss or alteration of river corridor habitats will have consequences for biodiversity and ecosystem services. A mosaic of habitat types with differing levels of connectivity and multiple transition zones between habitats will provide maximum biodiversity and allow for recovery of taxa after hydrological extremes.