papers on the measurement, modelling and adaptive management of inputs from coastal catchments draining into Australia's World Heritage-listed Great Barrier Reef. The papers are organised following the key components of a water quality improvement plan. First, the key pollutants and their critical sources are identified through a series of studies on water quality monitoring and modelling. Second, land-use and management-practice patterns that most cost-effectively achieve specified pollutant load targets are explored. Third, the planning frameworks and processes for water quality management are evaluated in the context of decentralised approaches to complex environmental management issues. The final paper of this special issue synthesises the main research findings and places them into an international context and provides recommendations for future research.