Dynamics of flooding and drying resulting in fragmentation of lotic habitats are a yearly phenomenon in subtropical floodplain rivers but their ecological significance is not known for invertebrate communities. We studied the response of zooplankton and macroinvertebrate communities in 48 dry-season river pools in the Save-Runde river system (Lowveld, Zimbabwe). Patterns and ecological processes influencing invertebrate communities, taxon richness and macroinvertebrate functional richness were investigated with focus on the role of regional (connectivity) and local processes (habitat characteristics). Local factors accounted for 15% of the variability in the zooplankton community but only 3.4% for the macroinvertebrate community. Important factors affecting zooplankton densities in the pools were depth, vegetation cover and presence of fish (planktivorous and omnivorous). The presence of fish in pools can infer predation risk. Macroinvertebrate abundances were affected by the presence of fish only. Zooplankton densities increased in pools with fish while macroinvertebrate densities declined in the presence of fish. Macroinvertebrates could exert top-down pressure on zooplankton either by competition for resources or predation in pools. Regional factors significantly explained zooplankton but not macroinvertebrate community variability. Connectivity had no significant effect on local pool habitat characteristics. There were no significant differences in water quality variables between flowing river sites and the pools. Zooplankton and macroinvertebrate alpha- and gamma-diversity in dry-season pools was higher than in the flowing river. Species additions rather than species replacements by processes that include dispersal and possibly dormancy may explain increased zooplankton and macroinvertebrate taxon diversity in pools. Functional feeding group (FFG) analysis showed that the proportion of macroinvertebrate predator taxa increased significantly in pools compared to the flowing river. Pools create a more suitable and diverse habitat for these widely dispersing taxa. The other FFG were comparable between the river and pools. The pools are strongly heterotrophic. Our results confirm that habitat fragmentation may actually be beneficial for zooplankton and macroinvertebrate biodiversity in dryland rivers.