• Freshwater and estuarine ecosystems are among the most threatened In the world, are under-represented In Protected Area Policies and have the highest portion of species threatened with extinction. • Freshwater biodiversity is particularly threatened because its conservation depends on: maintaining hydrological processes; retaining longitudinal connectivity of water flows without barriers along rivers; conserving lateral connectivity between a water body and its floodplain; sustaining adequate groundwater-surface water interactions; managing exogenous threats that are propagated across catchments; and Integrating governance by multiple management authorities. The impacts of agriculture, aquaculture and fishing need to be managed. • Where PAs are established particular attention should be given to: minimising impacts of water infrastructure, Invasive species incursion control; reducing impacts of visitor facilities and activities; and pollution prevention. • Floods, droughts and fire are natural processes in many freshwater eco-­systems and plants and animals can normally tolerate or recover from them. However, these processes are increasingly exacerbated by climate change leading to changes in ecological character. In different circumstances freshwater ecosystems may attenuate or increase the impacts of natural disasters on people.