Current work on adaptation responses for conservation management in the face of predicted climate change has a distinctly terrestrial focus. Existing evidence for the potential impact of climate change on freshwater ecosystems indicates that it is the interaction between direct climate change and current anthropogenic pressures that is likely to define the way in which freshwater biodiversity is affected. A brief overview of the likely effect of climate change upon fresh waters is presented. In light of this review, possible actions to safeguard freshwater biodiversity in the face of climate change are discussed. Management challenges and proposed responses are presented at the level of individual sites, at the landscape scale and according to management policy drivers. Many of the principles underlying these proposed adaptation responses need a more extensive and robust evidence base and an attempt is made here to highlight the key research gaps.