In the 1920s, a series of main-channel weirs were installed along Australia’s Murray-Darling Basin river system. Since then, hundreds of additional regulating structures have been added, and today up to 61% of water flow is extracted each year. Within a century, this dynamic boom-and-bust river system has been coerced into a sluggish, single channel that is largely disconnected from its floodplains and wetlands. This major environmental shift is driving the decline of many species, including the southern bell frog (Litoria raniformis). The Water Act 2007 is world-leading policy that ensures the riverine environment ‘owns’ a proportion of its annual flow. Under the Act, this water is delivered to strategic locations to achieve positive ecological outcomes; however, the rationale behind delivery is often lacking. To guide the delivery of water for southern bell frog conservation, we built stochastic hydroecological population models and found that the shift from natural to regulated flow conditions was the principal driver of southern bell frog declines in this reach. We refined the models to simulate a virtual network of 23 wetlands along 70 km of the Murray River (between Locks 2 and 3), which we populated with a metapopulation of southern bell frogs that could move between wetlands. We exposed the model to a range of water-management scenarios and used millions of stochastic iterations to determine which scenarios performed best. We found that the spatial configuration of water delivery sites influenced the metapopulation response and that effective management strategies can support the population through catastrophic drought conditions. This modelling approach can be adapted to a range of wetland species and can guide the efficient and effective use of limited water resources to achieve conservation targets.