This study uses species distribution modeling and physiological and functional traits to predict the impacts of climate change on native freshwater fish in the Murray-Darling Basin, Australia. We modelled future changes in taxonomic and functional diversity in 2050 and 2080 for two scenarios of carbon emissions, identifying areas of great interest for conservation. Climatic-environmental variables were used to model the range of 23 species of native fish under each scenario. The consensus model, followed by the physiological filter of lethal temperature was retained for interpretation. Our study predicts a severe negative impact of climate change on both taxonomic and functional components of ichthyofauna of the Murray-Darling Basin. There was a predicted marked contraction of species ranges under both scenarios. The predictions showed loss of climatically suitable areas, species and functional characters. There was a decrease in areas with high values of functional richness, dispersion and uniqueness. Some traits are predicted to be extirpated, especially in the most pessimistic scenario. The climatic refuges for fish fauna are predicted to be in the southern portion of the basin, in the upper Murray catchment. Incorporating future predictions about the distribution of ichthyofauna in conservation management planning will enhance resilience to climate change.