The biodiversity hotspot of southwestern Australia is predicted to experience considerable reduction in precipitation and increases in temperature as a result of climate change. This is likely to result in contractions and or shifts in species distributions for a number of taxa. Eleven species of freshwater fishes are known in southwestern Australia, nine of which are endemic to the region. It is anticipated that climate change will have pronounced effects on the climate envelopes of these species. In this study, we use species distribution modelling to identify priority areas for fish habitat restoration and conservation in southwestern Australia. Areas were identified by overlapping the future suitable climate envelopes of the species, with a greater number of overlapping areas indicating higher priority. Individual species’ exposure to climate change was measured by proportion of occurrence records located within the area which current and future climate envelopes overlap, a low proportion indicating higher exposure to climate change. The implications of these priority areas for management of freshwater fish in the region are discussed.