Five high level ecological principles common to all freshwater ecosystems are presented. Although they have different ramifications for each ecosystem type these principles are fundamental to the design and management of all freshwater protected areas (PAs) and the conservation of aquatic biodiversity. Freshwater ecosystems, often referred to as freshwater wetlands, encompass many different types, geomorphic forms and sizes and have been defined and classified in different ways, although not all efforts are systematic or readily comparable. A universal guiding principle for PA management is that the entire catchment with its land, water, biogeochemical resources and processes is the ideal unit to be protected and managed. Management plans targeting the catchment scale can offer opportunities for protected-area managers to favourably influence stakeholders and neighbouring land use, as well as promoting resilient ecosystems and ecosystem services. Freshwater species have long histories of exposure and adaptation to variable environmental conditions and extremes, conferring resistance and resilience at the individual, community and ecosystems levels.