Rivers flowing into the Great Barrier Reef carry contaminants such as suspended sediments, dissolved inorganic nitrogen, total phosphorus and pesticides. To measure the extent and direction of the contaminants after they enter the Great Barrier Reef lagoon, a model was created using river volume, flooding variability, contaminant load, distance and direction as inputs. A GIS was used to calculate and visualise the exposure of the contaminants to the reefs for the current day, as well as modelling scenarios for pre-European arrival loads, and land management using realistic targets set by a regional Natural Resource Management board for water quality improvement planning purposes. The results show that a reduction in the dissolved inorganic nitrogen load exiting the Tully and Murray Rivers reduces the exposure of reefs close to the basin, but that reefs further east of the basin are significantly influenced by other rivers, highlighting that management for water quality improvement in neighbouring basins is also required.