The presence of water in semi-arid environments is both spatially and temporally unpredictable and variable, creating a harsh and patchy environment. When present, water stimulates the germination and growth of plants but can also result in plant (or seedling) mortality. This study investigates how seedling emergence and mortality differ between various key habitats in a semi-arid floodplain wetland complex that are characterised by contrasting wetting regimes. Sediment samples were collected from five habitats (red soils, box-hollows, riparian areas, floodplains and lakes) and used in a germination experiment. Over a 12 week period, each habitat (except lakes) showed a peak in seedling emergence in the second week after initial experimental wetting, with boxhollows showing the largest emergence response in all weeks and riparian areas showing the lowest mortality (as a percent of emerged plants). Meanwhile the lowest overall emergence occurred in lakes and the highest mortality was found in red soils. Each habitat displayed a unique emergence and mortality response over the 12 weeks of the experiment suggesting that habitat has a strong influence on seedling emergence and survivability.