Lateral hydrological connectivity differentially affects the community characteristics of multiple groups of aquatic invertebrates in tropical wetland pans in South Africa

River–floodplain connectivity (i.e. lateral hydrological connectivity, LHC) can directly affect the community characteristics by promoting dispersal of organisms but can also have profound indirect effects by altering local habitat characteristics. A major challenge is to disentangle the relative importance of direct and indirect effects of LHC on organisms. Combining taxonomic data with trait information allows a more mechanistic understanding of how LHC affect biotic communities in floodplains. Here, we attempted to determine the relative importance of the direct and indirect effects of LHC on local environmental variables and community characteristics (taxonomic and trait composition) of three different taxonomic organism groups in a set of 33 temporary floodplain pans along a gradient of LHC. In addition, we specifically aimed to unravel the underlying mechanisms shaping patterns of taxonomic diversity by partitioning compositional dissimilarity between ponds into components of nestedness and spatial turnover. Variation partitioning revealed that most differences in macroinvertebrate and zooplankton community composition between pans resulted from variation in local environmental variables, particularly macrophyte cover and the presence of fish. For large branchiopod crustaceans, however, partitioning indicated that LHC did significantly affect both taxonomic and trait community composition, and reduced local taxon diversity. Partitioning taxonomic and trait β-diversity showed that community dissimilarity between pans was largely determined by turnover, rather than by nestedness. Overall, our study revealed that the effects of LHC on aquatic invertebrate communities act mainly indirectly by altering local environmental conditions. Although the effects of LHC were significant, they were small compared to those of environmental variables. Our results from the partitioning of taxonomic and trait β-diversity have important implications for biodiversity conservation efforts in the Ndumo region. We demonstrate the need to conserve multiple pans along the LHC gradient to sustain high regional diversity. A common practice in the study area mainly focuses on the conservation of river-connected or larger pans.