River flows in the Murray'Darling Basin, as in many regions in the world, are vulnerable to climate change, anticipated to exacerbate current, substantial losses of freshwater biodiversity. Additional declines in water quantity and quality will have an adverse impact on existing freshwater ecosystems. We critique current river-management programs, including the proposed 2011 Basin Plan for Australia's Murray'Darling Basin, focusing primarily on implementing environmental flows. River management programs generally ignore other important conservation and adaptation measures, such as strategically located freshwater-protected areas. Whereas most river-basin restoration techniques help build resilience of freshwater ecosystems to climate change impacts, different measures to enhance resilience and reoperate water infrastructure are also required, depending on the degree of disturbance of particular rivers on a spectrum from free-flowing to highly regulated. A crucial step is the conservation of free-flowing river ecosystems where maintenance of ecological processes enhances their capacity to resist climate change impacts, and where adaptation may be maximised. Systematic alteration of the operation of existing water infrastructure may also counter major climate impacts on regulated rivers.