The effects of climate and land-use change, coupled with limited management resources, mean that managers are increasingly faced with decisions to invest in some locations at the expense of others. Given their potentially controversial nature, such decisions require predictions of likely outcomes under different management strategies and potential future climates. We develop an approach to prioritise management interventions across multiple locations in highly variable and uncertain environments, using a stochastic model of population dynamics structured to include the (dynamic) effects of environmental conditions on key vital rates. We demonstrate this approach with a case study on the endangered Australian freshwater fish, the Macquarie perch (Macquaria australasica), assessing the effectiveness of seven management interventions under five scenarios of deterministic climate change. All management interventions were predicted to improve Macquarie perch population outcomes (increased abundances, reduced risk of quasi-extinction), with the risk of declines lowest when management included augmented gene flow and enforcement of fishing regulations. The lowest levels of risk occurred in locations with stable environmental conditions, which suggests that reintroducing Macquarie perch to large, regulated rivers with suitable access to spawning habitat may be more beneficial than investment in small, unregulated streams where populations were unlikely to persist under any scenario. Population reintroductions provide opportunities to shift populations from water-stressed to water-secure locations where required (e.g. to preserve unique genetic diversity). This finding likely applies to many aquatic species, and highlights a potential need to supplement threat mitigation in water-stressed locations with efforts to establish new populations in water-secure locations.