1. Floodplain wetlands are areas of high biodiversity and conservation value, including those in semi-arid regions. River regulation has resulted in disconnection from the main river channel of several ephemeral wetland systems, with profound modifications to their natural wetting/drying cycles that have contributed to the decline in diversity, distribution and abundance of native fish. 2. From 2005 to 2011, a series of managed inundation events through pumping followed by natural inundation allowed assessment and comparison of the fish assemblage developing in Hattah Lakes, a semi-arid wetland system of the regulated Murray River (Victoria, Australia). 3. As a result of one-way pumping from the main channel to Hattah Lakes, a ‘filtered’ fish assemblage consisting mainly of small-bodied native species and very low numbers of non-native species fully developed within 2 years. After disconnection from the main river channel in the absence of pumping, within-system recruitment also occurred, but later drying of all water bodies caused the entire fish assemblage to perish. Conversely, following two-way flooding by natural inundation a more diverse fish assemblage developed, including large-bodied native species but also non-native species, some of which were previously unrecorded. 4. Managed inundation through pumping in Hattah Lakes represents a viable option for the creation of fish habitat, for promoting recruitment, and as a measure of rehabilitation. However, the absence of connectivity back to the main river channel means that future measures should be implemented to maintain a refuge water pool until the next inundation event. Long-term monitoring is a key component of the integrated wetland conservation framework adopted by the Ramsar Wetland Convention, and this is especially relevant to the conservation of semi-arid wetlands world-wide including Hattah Lakes.