Soil seed banks are an important component of plant community diversity in ephemeral wetlands, allowing many species to persist through unpredictable periods of flood and drought. Spatial variation of extant vegetation in such habitats commonly reflects patterns of flood history and often varies predictably between broadly differing hydro-geomorphic habitat types. Here we investigate whether spatial variation of soil seed banks is similarly controlled by fluvial processes at this scale. Results are presented from a seedling emergence trial using samples collected from a range of habitat types, and at different scales within these, in the ephemeral Narran Lakes system in semi-arid Australia. Composition and structure of soil seed banks varied significantly between habitat types reflecting broad differences in flood frequency. As predicted, germinable seed abundance was found to be highest in intermediately flooded habitats. Variability in soil seed bank composition at a local scale was also found to be influenced by hydrology with greater spatial heterogeneity evident in the river channel as well as amongst the least frequently inundated riparian and floodplain habitats.