Plant species in temporary wetlands can be subject to dramatic changes in conditions, ranging from prolonged inundation to prolonged drought. Temporary wetland plants exhibit a range of mechanisms which facilitate persistence through periods of extreme dry and/or extreme wet including long-lived soil seed banks which tend to be particularly prevalent in dryland regions. This study examines responses of vegetation and soil seed banks to a managed flood in wetlands on a lowland river floodplain in semi-arid Australia using a Before-After/Control-Impact design (BACI). The main aim of this work was to investigate the role of soil seed banks in vegetation responses to flooding following an extended dry period. Differences in extant vegetation after flooding were clear from the first post-flood survey (approximately 2 months after flooding) and persisted until the final survey almost 12 months after inundation. In contrast, no differences were evident between the germinating assemblages from the soil seed bank of flooded and not flooded sites. Germinating assemblages did however differ significantly from extant assemblages, although this difference reduced over time. We hypothesize that the initial, rapid vegetation response to flooding was facilitated by vegetative reproduction from dormant rhizomes of Eleocharis sphacelata, the dominant taxon in flooded wetlands, which was rare in germinating assemblages. Our results suggest, however, that the contribution of the soil seed bank to the vegetation assemblages of flooded wetlands increased over time, as flood waters receded, and provided the principal source of the gradual increase in plant species richness observed in post-flood vegetation.