Microcrustacea in ephemeral wetlands produce dormant eggs to escape prolonged dry conditions. These eggs can hatch on inundation, although in most cases not all eggs hatch during a single wetting event. Incomplete hatching can reflect bet-hedging strategies, but also the presence or absence of environmental cues that stimulate hatching. This study examines the effects of environmental cues likely to change for wetlands in the future, namely, temperature and water depth. Surface sediments collected from dry anabranches of the Macintyre River floodplain (eastern Australia) were inundated under two temperature regimes (warm and cool) in microcosms of two depths (shallow and deep). Hatched microcrustacea were sampled for 6 weeks. The abundance and assemblage composition of microcrustacea varied by temperature but not by depth. Although the total abundance was greater under warm conditions, the effect of temperature diminished over time. Temperature also had a greater effect on non-ostracods, with 144% more non-ostracods being hatched under warm than under cool conditions. Thus, changes to temperature during inundation periods arising from global climate change or river regulation are likely to influence the abundance and composition of microcrustacean assemblages, especially among non-ostracods, which will influence food availability for larval and juvenile native fish and, hence, recruitment.