Salt is a natural component of the Australian landscape to which a number of biota inhabiting rivers and wetlands are adapted. Under natural flow conditions periods of low flow have resulted in the concentration of salts in wetlands and riverine pools. The organisms of these systems survive these salinities by tolerance or avoidance. Freshwater ecosystems in Australia are now becoming increasingly threatened by salinity because of rising saline groundwater and modification of the water regime reducing the frequency of high-flow (flushing) events, resulting in an accumulation of salt. Available data suggest that aquatic biota will be adversely affected as salinity exceeds 1000 mg L–1 (1500 EC) but there is limited information on how increasing salinity will affect the various life stages of the biota. Salinisation can lead to changes in the physical environment that will affect ecosystem processes. However, we know little about how salinity interacts with the way nutrients and carbon are processed within an ecosystem. This paper updates the knowledge base on how salinity affects the physical and biotic components of aquatic ecosystems and explores the needs for information on how structure and function of aquatic ecosystems change with increasing salinity.