Australia's large desert floodplains are among the world's most hydrologically variable wetlands and vegetation in these habitats changes dramatically over time in response to flooding and drought. Annual forb and grass communities in these desert floodplains rely on large, diverse soil seed banks as critical sources of propagules for recruitment. I investigated the effects of flooding on seedling emergence from the soil seed bank of the Cooper Creek floodplain in arid central Australia. My objective was to determine the effects of differences in both short-term flooding characteristics as well as the longer-term flood history of sediments on the composition of plant communities establishing from the soil seed bank. I conducted a greenhouse experiment in which sediments collected from high (inundated at least once every 1–5 yrs), medium (inundated approximately once in every 5–10 yrs), and low (inundated less than once a decade) flood frequency zones were subjected to different durations of submergence, rates of drawdown (i.e., duration of post-submergence waterlogging), and seasonal timing of flooding. The abundance of emerging seedlings more than doubled in response to longer overall durations of wetting, but the relative duration of submergence (i.e., 8 vs. 4 weeks) versus subsequent soil waterlogging (i.e., 4 vs. 8 weeks) within this period did not have a significant effect. The duration of submergence versus waterlogging did however influence the composition of emerging seedlings with almost twice as many annual monocots appearing following longer durations of submergence. All dominant species emerged frequently following both summer and winter flooding, suggesting opportunistic germination strategies. The composition of moderately abundant and rare species, however, differed in response to the seasonal timing of inundation with monocots more common following summer floods and forbs following winter flooding. Common species were well-distributed in the soil seed bank across the flood history gradient, and the species richness of emerging seedlings did not vary between different flood frequency zones. However, seedlings of species emerging from low flood frequency zone samples tended to be less abundant and differed in composition compared with those emerging from samples of high and medium flood frequency zones. My results suggest that changes to both short- and long-term flooding patterns, through flow management or climate change, are likely to affect vegetation responses to inundation in these desert floodplains. Reductions in flood pulse magnitude and frequency, for instance, could result in a decline in the abundance of valuable pasture grasses germinating in response to summer flooding and a loss of hydrophytic species in rarely flooded areas.