Decentralised approaches to water governance have emerged as a common approach to tackle complex environmental management issues in Australia and elsewhere. While decentralisation offers hope for a more holistic, integrated and effective approach to environmental planning decisions and solutions, challenges remain to put these ideals into practice. The present paper focuses on a key component of this approach to environmental planning and decision-making – the integration of different types of knowledge used to inform planning goals and the design of water quality management programs. The analysis draws on knowledge integration issues surrounding the water quality improvement plan in the Tully–Murray basin in north-eastern Australia. Here, government and non-government stakeholders are coordinating efforts to assess water quality condition and set management priorities for improving the quality of water entering the Great Barrier Reef World Heritage coastal lagoon. Our analysis of the kinds of knowledge and mechanisms of translation involved highlights three main points. First, the tensions between the uncertainty and bias in different types of knowledge brought to the planning table. Second, the timing of knowledge contributions that affects if and how knowledge contributions can be debated and integrated. Finally, the challenges faced by local collaborative groups to broker the translation and integration of knowledge needed to inform strategic environmental decisions and programs.