Clearing of native vegetation and replacement with cropping and grazing systems has increased nutrient exports to the Great Barrier Reef (GBR) to a level many times the natural rate. We present a technique for modelling nutrient transport, based on material budgets of river systems, and use it to identify the patterns and sources of nutrients exported. The outputs of the model can then be used to help prioritise catchment areas and land uses for management and assess various management options. Hillslope erosion is the largest source of particulate nutrients because of its dominance as a sediment source and the higher nutrient concentrations on surface soils. Dissolved nutrient fractions contribute 30% of total nitrogen and 15% of total phosphorus inputs. Spatial patterns show the elevated dissolved inorganic nitrogen export in the wetter catchments, and the dominance of particulate N and P from soil erosion in coastal areas. This study has identified catchments with high levels of contribution to exports and targeting these should be a priority.