Climate change poses a severe global threat to freshwater ecosystems. Aestivating freshwater fauna (i.e., those that undergo periods of dominancy during dry periods) are likely to be highly susceptible to climate change due to their unique life-cycles, although empirical data that demonstrates this are lacking. This study utilised two aestivating fishes as model species, the salamanderfish, Lepidogalaxias salamandroides, and the black-stripe minnow, Galaxiella nigrostriata; both of which are endemic to Australia's Southwestern Province, an area undergoing a severe drying trend that global climate models project will continue. We found that the distributions of both species have undergone large reductions in extent of occurrence (EOO) and area of occupancy (AOO), coinciding with an extensive period of severe drying of the region. L. salamandroides was more likely to be found in deeper pools, while G. nigrostriata was found more often in pools with greater connectivity, and the probability of occurrence of both species was significantly associated with lower water temperature and pH, and higher oxidation-reduction potential. The majority of those factors are strongly influenced by the local climate, as stable isotope analyses found the hydrology of the pools in which they occurred was influenced by winter rainfall, either through direct input and/or expression from a superficial aquifer. This suggests that increasing water temperature and declining rainfall, features of the climatic shift in south-western Australia over the last 40. years, have been the major drivers of the observed declines in range. Given that climate models project both continued rainfall reductions within the species' distributional ranges and water table decreases by up to 4. m by 2030, further population losses are expected. Moreover, a review of the distribution of aestivating fish species throughout the world revealed that 75% are found in regions projected to dry due to climate change. This has considerable management implications, and active intervention, such as the protection of their existing environments and the creation of new suitable habitats, is required to prevent species declines. Fortunately, at least for the two aestivating species found in Western Australia, artificial ponds are utilised and therefore the construction of new waterbodies could help halt their decline, although further research is required to develop the optimal design for species persistence.