Global biodiversity hotspots contain exceptional concentrations of endemic species in areas of escalating habitat loss. However, most hotspots are geographically constrained and consequently vulnerable to climate change as there is limited ability for the movement of species to less hostile conditions. Predicted changes to rainfall and temperature will undoubtedly further impact on freshwater ecosystems in these hotspots. Southwestern Australia is a biodiversity hotspot and, as one of the first to experience significant climate change, is an example and potentially a global bellwether for issues associated with river restoration. In this hotspot, current and predicted water temperatures may exceed thermal tolerances of aquatic fauna. Gondwanic aquatic fauna, characteristic of southwestern Australia, are typically cold stenotherms and consequently intolerant of elevated temperatures. The hotspot in southwestern Australia is geographically restricted being surrounded by ocean and desert, and many important national parks are located on the extreme south coast, where the landscape is relatively flat. Consequently, fauna cannot change their distribution southwards or with altitude as a response to increasing temperatures. Therefore, any mitigation responses need to be in situ to produce a suitable biophysical envelope to enhance species’ resilience. This could be through “over restoration” by increased riparian replanting at a catchment scale. A rule-of-thumb of a 10% increase in riparian cover would be required to reduce water temperatures by 1°C. These restoration techniques are considered applicable to other global biodiversity hotspots where geography constrains species’ movement and the present condition is the desired restoration endpoint.