Information on species diversity and distribution of aquatic microfauna such as Rotifera, Cladocera, Copepoda and Ostracoda across wetlands can assist with interpreting wetland processes, water sources and hydrological connections, and water quality. We sampled the aquatic microfauna from 36 wetlands across the Lachlan catchment divided into semi-arid, temperate inland and temperate upland zones. Among over 100 species of aquatic microfauna recorded overall, one notable aspect was the occurrence of two Tasmanian rotifer species of Brachinus lyratus tasmaniensis and Lepadella tyleri in the semi-arid zone. This raises intriguing questions about possible dispersal and biogeographical distribution. Migratory waterbirds may be important as potential vectors of microfauna, as has been suggested for the Macquarie Marshes, another large floodplain wetland in the Murray-Darling Basin of south-eastern Australia. We conclude that the conservation and maintenance of diverse wetland habitats across different geographical zones should ensure the survival, diversity and effective dispersal of the microfauna and help maintain the ecological structure and function of the Lachlan wetlands.