To reduce sediment exports discharging to the Great Barrier Reef (GBR), it is essential to identify the sources of exported sediment. We used modelling of spatial sediment budgets (the SedNet model) to identify sources and deposition of sediment as it is transported through river networks. Catchments with high levels of land clearing, cattle grazing and cropping show the largest increases in sediment export compared with natural conditions. Hillslope erosion supplies 63% of sediment to the rivers. Gully erosion and riverbank erosion are lower sources of sediment at the GBR catchment scale, but they are important in some catchments. Overall, 70% of sediment exported from rivers comes from just 20% of the total catchment area, showing that much of the problem can be addressed in a relatively small area. This is a much more manageable problem than trying to reduce erosion across the entire GBR catchment. Areas of high contribution are all relatively close to the coast because of the high erosion and high sediment delivery potential.