A risk assessment method was developed and applied to the Great Barrier Reef (GBR) to provide robust and scientifically defensible information for policy makers and catchment managers on the key land-based pollutants of greatest risk to the health of the two main GBR ecosystems (coral reefs and seagrass beds). This information was used to inform management prioritisation for Reef Rescue 2 and Reef Plan 3. The risk assessment method needed to take account of the fact that catchment-associated risk will vary with distance from the river mouth, with coastal habitats nearest to river mouths most impacted by poor marine water quality. The main water quality pollutants of concern for the GBR are enhanced levels of suspended sediments, excess nutrients and pesticides added to the GBR lagoon from the adjacent catchments. Until recently, there has been insufficient knowledge about the relative exposure to and effects of these pollutants to guide effective prioritisation of the management of their sources.