The rivers and coastal waterways of South East Queensland, Australia, represent unique and complex ecosystems that have a high conservation value and support major recreational and commercial fisheries. The agricultural districts of the region also contribute significantly to the local economy and, together with the growing urban areas, are heavily reliant on good quality water supplies. However, urban and rural development has led to significant changes in catchment hydrology and sediment delivery, declining water quality and loss of aquatic biodiversity. Predicted population increases in the region are likely to further impact on the ecological and economic health of its waterways and catchments, and there are growing community expectations to reverse the decline in water quality and ecosystem health. In response to these concerns, government, industry and community stakeholders have worked in close cooperation to develop a whole-of-government, whole-of-community approach to understanding and managing the region’s waterways. The key elements of the Healthy Waterways Partnership include: the implementation by a range of partners of management actions ranging from upgrades of sewage treatment plants to improved planning regimes and rehabilitation of riparian vegetation; a multi-disciplinary science and research program that underpins the management action program and monitors its effectiveness; and the Healthy Waterways promotional and educational program that seeks to build on similar activities of partners and ensure that there is community awareness and support for action. This paper provides an overview of the experience gained through development of the Partnership and highlights some of the key factors we believe have contributed to its current success.