Temporary lakes play a vital habitat role in the semi-arid zone of the Murray-Darling Basin. Aquatic microcrustacea and aquatic plants persist in dry lake beds by virtue of resting propagules: eggs and seeds. As lakes fill, microcrustacea and plants emerge, providing an important food source for larger animals including waterbirds, frogs and fish. As waters recede, resting propagules are deposited. The status of cryptic propagules across dry lakebeds in relation to inundation regimes, with implications for ecosystem foodwebs, is poorly understood. Under a drier future, spatial filling extent, duration and frequency may be reduced in Australia’s semi-arid zone, leaving some propagules high and dry. We examined differences in microcrustacea and plant biomass emerging from sediments across a gradient from lake centres to shorelines to determine patterns in biomass, abundance and diversity. We used an ex-situ setup of microcosms from five temporary lakes in the Paroo Basin of north-western NSW. There were differences in microcrustacea and aquatic plants at different filling levels. The results have implications for the effects of climate change on aquatic organisms, and are also relevant for environmental flow management in the Murray Darling Basin. These results can inform flow duration and frequency in relation to a key component of the foodweb: aquatic microcrustacea and plants.