Policy and programs currently in place in Australia for the protection of freshwater biodiversity are discussed, primarily within the context of the frameworks provided by key international, national and State strategies. The paper identifies three important gaps in existing programs at Commonwealth and State levels: (a) a failure by State governments to develop comprehensive and effective programs to manage the cumulative effects of incremental infrastructure development, (b) the completion of comprehensive State wide freshwater ecosystem inventories, and (c) programs to develop representative freshwater ecosystem reserves.