Background/Question/Methods Freshwater ecosystems are regarded as the most threatened on the planet and further declines in freshwater biodiversity are predicted, largely as a consequence of an expanding human population but also driven by (or at least exacerbated by) climate pressures. We anticipate some direct climate-driven impacts to Australia’s freshwater biodiversity in the medium to long-term, through losses of coastal wetland habitats from rising sea level and from the impacts of increased water temperatures on species already living close to their thermal optima. Increased hydrological variability, higher evaporation rates and severity of droughts will have more pervasive effects by reducing the spatial and temporal distribution of aquatic refugia. These direct threats may be overshadowed in the short term as governments attempt to drought proof cities and divert more water to meet agricultural needs. Results/Conclusions It is unlikely that current water management practices will be adequate to fully mitigate the negative impacts of climate change on freshwater ecosystems. There is an urgent need to understand the risks to Australia’s freshwater biodiversity due to climate change (in the context of other pressures) as well as the technical and policy interventions that will be required to meet future human water needs without further degrading freshwater ecosystems and the important natural assets and values they provide. To help address these issues, a “Water resources and freshwater biodiversity” network of researchers and water managers has been established as one of eight themes under the newly formed Australian National Climate Change Adaptation Facility (www.nccarf.edu.au).