Freshwater ecosystems (including inland saline wetlands and mound springs) are among the more imperilled ecosystems in the world. Australia is no exception, but their protection has lagged behind programmes of terrestrial protection. Freshwater protected areas are an essential component of biodiversity conservation programmes, but a systematic approach to their development in Australia has been slow, and hindered by incomplete ecosystem inventories at State and national levels. We examine this problem and suggest avenues for action. Further, while there is no shortage of relevant legislation and policy for protecting freshwater aquatic systems in Australia, some protective mechanisms have not yet been used, many years after their development. In some places "protection" has been only partially applied without regard to important issues of hydrologic connectivity ? with species extinction as a direct consequence. The most urgent priority is to identify those aquatic ecosystems most at risk. A comprehensive national assessment of the conservation status of freshwater ecosystems should be undertaken immediately. Such an assessment would provide both a platform and an impetus for the systematic expansion of the nation's freshwater protected areas. Political will is then essential for effective conservation, utilizing the plethora of conservation and management tools available.