In 2014 the IUCN issued a call for a specific focus on the coverage and management of freshwater ecosystems in their own right rather than as components of protected areas (PAs) established for the protection of terrestrial ecosystems. Milton and Finlayson point out that freshwater ecosystems comprise a wide variety of types, such as rivers, lakes and swamps, and can be permanently, seasonally or intermittently flooded. Conservation efforts should extend into developing cooperative relationships and activities among various entities with overlapping water management mandates. Integrated and adaptive management approaches that facilitate engagement and empowerment of all stakeholders, inclusive and iterative learning, and purposeful action amidst inherent complexities, are recommended. The spatial and temporal connectivity patterns and processes of aquatic ecosystems in their natural state are important elements for consideration in PA design and management. The widely anticipated impacts of climate change on freshwater ecosystems add to the need for ensuring that PAs are effectively managed, and in an adaptive way.