Episodic inundation regulates germination and recruitment from soil seedbanks, which are key processes driving vegetation dynamics in dryland floodplains. In the Murray-Darling Basin, extensive floodplain modification and flow regulation have altered flow regimes so that anthropogenically controlled environmental watering is often required to replace natural floods. This presents challenges in delivering appropriate inundation events to generate desired ecological outcomes. We conducted a glasshouse experiment on floodplain soil seedbanks to test how inundation duration influences the germination of native and non-native plant species respectively. Seedbanks were exposed to a rainfall treatment (damp but unsaturated conditions), short inundation (14 days) or long inundation (28 days). These treatments were applied twice to capture responses to successive wetting, and therefore, the responses of seedbanks to repeated inundation. The findings demonstrate that inundation duration acts as an ecological filter, with longer flood duration favouring native species over non-native species. While plants of both native and non-native origin share disturbance-responsive traits that enable rapid germination and establishment following wetting, native species appear to be better able to tolerate longer periods of inundation than the non-native species present in the seedbank. Variation in flood duration is important for sustaining native vegetation, as many species are adapted to natural hydrological variability. Simultaneously, variable periods of inundation can reduce non-native recruitment, as many non-native seeds showed limited persistence after the initial inundation, either due to a loss of viability or exhaustion of seed stores. Native seeds, by contrast, remained viable through multiple inundation events. Therefore, periods of flooding, which can be substituted by environmental watering, can greatly benefit restoration and maintenance of native vegetation while providing the co-benefit of reducing non-native plant establishment from the soil seedbank.