The Fitzroy catchment is the largest Queensland catchment discharging to the Great Barrier Reef (GBR) lagoon. Sediments and nutrients together with anthropogenic pollutants originating upstream in the catchment are discharged from the Fitzroy River via the Fitzroy Estuary (FE) and ultimately into Keppel Bay (KB). The estuary and the bay act as natural chemical reactors where the materials delivered undergo chemical and physical transformations before some are deposited and stored in the growing deltaic and beach areas, with the remainder transported eastward to the southern zone of the GBR lagoon. The Reef Water Quality Protection Plan is a recent State–Commonwealth initiative which aims to improve land-use management practices within many Queensland catchments with the intent of reducing the loads of sediments, nutrients and other potentially deleterious substances entering the GBR lagoon. The background knowledge to make realistic predictions of the response of the FE and KB ecosystems to changed sediment and nutrient deliveries did not exist when this project started. The Agricultural Contaminants Project (Project AC) was developed to address these knowledge gaps and to produce a predictive framework to aid managers in the evaluation of various load reduction strategies.