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Aquatic ecosystems are connected over large spatial scales, have varied drivers, strong and often conflicting societal interests and interacting management processes. Many of the world’s protected areas (> 100,000, similar to 42% of land) include freshwater ecosystems, some specifically declared for freshwater protection, but often supplied by rivers outside their protected boundaries. Such complex socio-ecological systems have considerable challenges. We report on Strategic Adaptive Management (SAM), a management framework that should be implemented, irrespective of resourcing. in protected areas of any river system, ranging from heavily managed or regulated through to pristine rivers. We briefly outline the four stages of the SAM process for aquatic protected areas and present three case studies from South Africa and Australia in different stages of SAM implementation. Progress is incremental, reflecting gaps, problems, and socio-ecological dynamism. Real-world implementation usually means such management is passive although experimentation with environmental flows remains possible. While maturity in SAM is incremental over years or decades, it can and should be applied even if environmental problems are urgent and contentious. The stages of SAM should produce an agreed vision and/or mission among stakeholders, with an appropriate hierarchy of objectives that determines indicators to be measured, allowing ongoing reflection, learning and adaptation. There is no panacea for achieving aquatic conservation, but Strategic Adaptive Management offers hope with its interlinked processes for navigating complexity and learning. SAM in freshwater conservation is progressing because of the imperative for sustainability, history of interaction between scientists and managers and the need for transdisciplinary governance of rivers. (C) 2010 Published by Elsevier Ltd.