Climate change is expected to have significant impacts on hydrologic regimes and freshwater ecosystems, and yet few basins have adequate numerical models to guide the development of freshwater climate adaptation strategies. Such strategies can build on existing freshwater conservation activities, and incorporate predicted climate change impacts. We illustrate this concept with three case studies. In the Upper Klamath Basin of the western USA, a shift in land management practices would buffer this landscape from a declining snowpack. In the Murray–Darling Basin of south-eastern Australia, identifying the requirements of flood-dependent natural values would better inform the delivery of environmental water in response to reduced runoff and less water. In the Savannah Basin of the south-eastern USA, dam managers are considering technological and engineering upgrades in response to more severe floods and droughts, which would also improve the implementation of recommended environmental flows. Even though the three case studies are in different landscapes, they all contain significant freshwater biodiversity values. These values are threatened by water allocation problems that will be exacerbated by climate change, and yet all provide opportunities for the development of effective climate adaptation strategies.