Abstract. Australia's aquatic ecosystems are unique, supporting a high diversity of species and high levels of endemism; however, they are also extremely vulnerable to climate change. The present review assesses climate-induced changes to structural habitats that have occurred in different aquatic ecosystems. Climatic impacts are often difficult to discern against the background of habitat degradation caused by more direct anthropogenic impacts. However, climate impacts will become more pronounced with ongoing changes in temperature, water chemistry, sea level, rainfall patterns and ocean currents. Each of these factors is likely to have specific effects on ecosystems, communities or species, and their relative importance varies across different marine and freshwater habitats. In the Murray-Darling Basin, the greatest concern relates to declines in surface water availability and riverine flow, owing to declining rainfall and increased evaporative loss. On the Great Barrier Reef, increasing temperatures and ocean acidification contribute to sustained and ongoing loss of habitat-forming corals. Despite the marked differences in major drivers and consequences of climate change, the solution is always the same. Greenhouse-gas emissions need to be reduced as a matter of urgency, while also minimising nonclimatic disturbances. Together, these actions will maximise opportunities for adaptation by species and increase ecosystem resilience.