1. The factors that promote coexistence of global invaders and native species are poorly understood. The role of abiotic factors in determining the dominance of invasive species is also an area of increasing interest. Gambusia holbrooki (Eastern Mosquitofish) is an important global invader, displacing endemic fish and frogs on four continents. However, Gambusia co-occurs with a similar-sized fish (Hypseleotris spp.) in dynamic floodplain wetland pools of south-eastern Australia. 2. We examined the relative abundance of Gambusia and Hypseleotris in regularly flooded and irregularly flooded pools to determine whether seasonal hydrological disturbance may be advantageous to the native species. We aimed to determine whether Gambusia and Hypseleotris populations respond differently to regular seasonal flooding and whether this could reduce the ability of Gambusia to dominate numerically the native species. We tested this by sampling fish bi-monthly in 15 floodplain pools over 2.5 years. 3. We found that the relative abundance of the two species differed between regularly and irregularly flooded pools, while both pool types persisted (over a period of a year). Hypseleotris were numerically dominant in regularly flooded pools from spring through to autumn, following a major spring flood. In contrast, Gambusia were more abundant than Hypseleotris in irregularly flooded pools from summer until pools dried completely. 4. Due to the higher reproductive response of Hypseleotris to a spring flood, and the timing of its breeding season, we suggest that Hypseleotris may have a reproductive advantage over Gambusia during productive post-flood spring /summer conditions. While the abundances of both species were usually within a similar range, variation in hydrologic habitats and the inter-play between life-history traits and hydrologic disturbance may nonetheless give the native fish an edge.