Despite freshwater fishes being recognised as integral components of freshwater ecosystems, underpinning biodiversity, supporting food security, and contributing to the maintenance of ecological processes, globally they are in decline. The Murray hardyhead (Craterocephalus fluviatilis) is a salt tolerant, biologically resilient, wetland specialist fish endemic to the Murray-Darling Basin in southeastern Australia. The species has suffered severe declines in range and abundance and is listed as endangered nationally. Individuals of the species are short lived and extremely vulnerable to water management, flow modifications, habitat loss and impacts of invasive fish. We developed a stochastic population model with seasonal transition matrices based on the species complex life history to optimise the management of wetlands in which it persists or could be reintroduced. The frequency and timing of water deliveries to increase productivity of habitats were identified as critical for long-term population persistence. Reintroductions were predicted to be most successful accompanied by quantity and appropriate timing of water deliveries. Given productivity is a significant driver of recruitment, modelled scenarios showed spring inundations provided the highest population benefits, an outcome verified by field observations. This approach is easily transferrable to similar short-lived wetland species for improved risk assessment and optimizing management strategies.