The Wet Tropics region of north Queensland contains the highest biological diversity in Australia, has outstanding environmental values, is economically important and located adjacent to the Great Barrier Reef (GBR). Increasing urban development and agricultural intensification in the Wet Tropics has raised serious water quality concerns. To successfully achieve water quality improvement outcomes, the integration of social and biophysical knowledge, in particular clarifying the roles and responsibilities of multiple stakeholders for knowledge integration, has been identified as a key issue and research priority. However, research into the processes supporting knowledge integration and clarifying roles and responsibilities of multiple stakeholders for improving water quality is largely lacking. To fill this gap, we further developed and advanced a social-ecological planning framework to improve our understanding of how multiple-stakeholders can contribute to successful water quality management outcomes. Our conceptual framework, applied in the Tully basin adjacent to the GBR: (1) provides a transdisciplinary approach; (2) enhances the integration of social and biophysical knowledge through tailored methods fitting the local context; (3) shares knowledge and provides recommendations; (4) outlines factors that may promote or inhibit the implementation of freshwater quality objectives; (5) highlights inadequacies of existing government guidelines, policies, and presents co-management opportunities and (6) offers a novel collaborative approach supporting water quality improvement in the Wet Tropics of Australia and beyond.