Climate change and flow regulation are leading to the development of novel ecosystems that may require new thinking and a range of novel approaches to water management to cope with increasingly uncertain futures. By their nature, freshwater protected areas (PAs) tend to be focused on a specific locality with clearly demarcated boundaries, while successful management of PAs is normally expressed in terms of outcomes, compared with a reference state, and generally outlined in a management plan. A range of climate change adaptation interventions has been proposed to better conserve freshwater biodiversity in wetland PAs and river systems, including a set of options detailed in Australia. The development of an international policy framework for managing freshwater PAs in the face of climate change is seen as a necessary, but not the only step for ensuring such PAs are effective. Adaptation measures are also seen as necessary and will require a flexible and at times imaginative approaches to ensure they are effective.