Freshwater ecosystems are a foundation of our social, cultural, spiritual and economic well being. The degraded condition of many of Australia’s river ecosystems is testament to our failure to manage these resources wisely. Ecosystem science involves the holistic study of complex biophysical systems to understand the drivers that influence ecological pattern and process. Ecosystem science should underpin both water management and policy. Our understanding of aquatic ecosystems lags behind the increasing problems caused by past land and water management. Current post-graduate training programmes will not provide the aquatic ecosystem scientists needed by government and management agencies to prevent further degradation. We advocate new initiatives to capture the skills, knowledge and innovation of our research community by engaging scientists and managers in large-scale, long-term ecosystem science programmes across Australia and to integrate these programmes with community aspirations, policy, planning and management. We call on management agencies to increase their support for and uptake and use of ecosystem science. We also advocate establishment of national archives for long-term ecologically-relevant data and samples, and clear custodial arrangements to protect, update and facilitate knowledge-transfer. These initiatives need to be supported by more extensive, better-funded post-graduate and post-doctoral programmes in ecosystem science and management.