Freshwater ecosystems have very high biodiversity relative to their areal extent. They are particularly vulnerable to climate change because of their limited extent, their limited connectivity and, in much of Australia, their susceptibility to drying resulting from the high variability of temperature and rainfall. Identifying and managing freshwater refuges that will help protect Australian biodiversity from the impacts of climate change must be an important element of all future conservation planning and policy. Climatic stability is increasingly recognised as a key component of climate refuges, yet the identification of areas that combine relative future climatic stability with high biodiversity values has so far been elusive. Here we address this challenge by building ecological niche models (species distribution models) for multiple freshwater species (fish, crayfish, turtles and stream frogs) to identify broad-scale climate refuges as areas that minimise the impact of future climate change and are predicted to remain stable with respect to their freshwater species diversity. Substantial shifts in the distribution of environments suitable for freshwater taxa are predicted with highlands and upstream regions identified as important refuges for most taxa. For some taxa, areas of high instability overlap with areas currently notable for their high freshwater biodiversity values. This study presents the results of the first attempt to provide a continental-scale assessment of freshwater climate refuges across Australia.