The responses of zooplankton assemblages in arid zone rivers to seasonal changes, flow events, drying and water quality changes are fundamental to our understanding of these unregulated rivers. For three years the zooplankton and littoral microfauna in three rivers in the Lake Eyre Basin were studied. A diverse assemblage was discovered with a total of 398 identifiable taxa being recorded, consisting of 72 protist, 227 rotifer and 93 microcrustacean taxa. Zooplankton diversity was highest in a boom phase during, or in the summer following, a large flood. The rotifer assemblage dominated during, or soon after, periods of flow. However, during the winter and early summer, there was a decline in rotifer taxon richness and abundance accompanied by an increase in microcrustacean taxon richness and abundance. The winter samples occurred during the recession of a large flood and the early summer samples during periods of no flow. These changes suggested the involvement of a strong annual cycle of ecosystem structure evident within the longer term patterns of boom and bust driven by the timing and size of flood events. Multivariate and regression analyses found that salinity was a significant and independent driver of assemblage composition.