Approximately 40% of Australian freshwater fish species are of conservation concern, largely because of the impacts of river regulation, habitat fragmentation and alien fishes. Murray hardyhead is a threatened fish endemic to the southern Murray–Darling Basin in Australia, which has declined significantly in range and abundance since European settlement. Conservation of the species has relied largely on environmental watering of off-channel wetlands where isolated populations persist. This became problematic during recent drought (1997–2010) because of competing demands for limited water, and resentment towards environmental watering programs from communities that themselves were subject to reduced water entitlements. In response, emergency conservation measures prioritised the delivery of environmental water to minimise applied volumes. Captive maintenance programs were established for fish rescued from four genetically distinct conservation units, with varying levels of breeding success. Several translocations of wild and captive-bred fish to surrogate refuge sites were also conducted. Future recovery of the species should secure existing natural and stocked populations and translocate fish to additional appropriate sites to spread risk and reinstate natural pathways for dispersal. The approach to the conservation of Murray hardyhead during extreme environmental conditions provides insights to inform the management of fishes in other drought-prone regions of the world.