Effective water quality management requires knowledge that is scientifically sound, clearly communicated, and directly relevant to policy. As scientists our challenge is not only providing the information that meets these criteria, but doing so quickly and with existing resources. Here we outline our process of integrating different forms of knowledge including long term monitoring, literature reviews, data and spatial analysis, and expert opinion, to determine water quality status and major issues of importance. Using the Gwydir River as a case study we outline how both hydrology and catchment drivers are influencing water quality, and the challenges for natural resource managers.