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Traditionally, dispersal of aquatic invertebrates has been thought to be very closely associated with river network structure, despite many species being capable of active or passive dispersal across the terrestrial matrix. However, recent studies of both population genetics and community structure from dryland regions indicate that aquatic species commonly disperse across catchments, implying that movement away from streams is more common than originally thought. This study investigated how aquatic invertebrate metacommunity structure in central Australia is influenced by interactions between species’ dispersal traits, dispersal routes and local environmental conditions. We sampled community composition in 16 perennial and long-term inundated freshwater habitats in central Australia. Aquatic invertebrate taxa were allocated to one of four dispersal trait groups: obligate aquatic, passive aerial, weak flying and strong flying. We then used Mantel tests to examine correlations between trait group community dissimilarities, and four isolation models representing (i) local environmental conditions, (ii) geographical distances, (iii) landscape resistances restricted to river networks and (iv) landscape resistances incorporating overland dispersal conduits’. We found that the community composition of aquatic invertebrates in three of four dispersal trait groups, and all traits combined, was influenced primarily by topographic connectivity via overland dispersal conduits. Our results suggest that rainfall events and their effect on the landscape as a whole, rather than river flow during these events, shape aquatic invertebrate metacommunity structure in central Australia. This study provides further support for the importance of overland dispersal conduits to aquatic invertebrates, particularly in arid environments with irregular rainfall.