Increased regulation and extraction of water from rivers has contributed to the decline of fishes, and the use of environmental water allocations (EWAs) is now a key rehabilitation measure. Major reform of water policy in the Murray-Darling Basin (MDB), Australia, has recently provided significant EWAs to improve ecological outcomes. Conflict over water buybacks, the value of the water and the need to maximise environmental benefits and minimise risks of unwanted outcomes has increased the expectation for science to underpin and justify such actions. Recent research has focussed attention on the need to understand fish–flow relationships. The Native Fish Strategy for the Murray-Darling Basin 2003–2013 (NFS), while not specifically targeted at water policy reform or water delivery, has provided fish ecology research and flow restoration experimentation and contributed considerable new scientific knowledge to support flow management. It has contributed to a substantial and positive change in environmental watering for fish, with native fish targets now regularly incorporated into watering objectives. This study documents changes to water management in the MDB, summarises current knowledge of flow-related fish ecology in the MDB, highlights the benefits and risks of some water management practises and provides recommendations for future management and research. A major recommendation is the need for a coordinated, cross-jurisdictional approach to flow restoration for native fish, ensuring that the best available science is being used in all watering allocations. We caution on the use of environmental works such as regulators to artificially inundate floodplains and suggest that such approaches should be viewed as large-scale experiments with the significant risks posed to fish needing to be recognised, adequately monitored and adaptively managed.