The abundance and richness of macroinvertebrates in the lower Murray and Darling rivers were examined at a macroscale (rivers), mesoscale (billabongs, backwaters, channel) and microscale (vegetation, snags, substrata). In the Darling, insects dominated (85% of taxa, 81% of individuals); the richest taxa were Diptera (26 taxa) and Coleoptera (15 taxa) and the most abundant were Hemiptera (47%) and Diptera (35%). In the Murray, insects again dominated (84% of taxa, 52% of individuals), particularly Diptera (22 taxa), Coleoptera (12 taxa) and Hemiptera (9 taxa), but there were more crustaceans (9% of taxa, 47% of individuals, particularly the atyid shrimp Paratya australiensis). Both assemblages were uneven: in the Darling, >50% of biomass was Micronecta spp. (Corixidae), Dicrotendipes sp. (Chironomidae) and Macrobrachium australiense (Palaemonidae); in the Murray, 70% of biomass was P. australiensis and Caridina mccullochi (Atyidae) and the insects Micronecta spp. (Corixidae) and Chironomus sp. (Chironomidae). Abundances generally were greatest in the Murray. Hydrologic and geomorphic factors influenced assemblages at the macroscale, whereas microhabitat diversity dominated at the mesoscale.