The Great Barrier Reef (GBR), situated off the coast of Queensland, is Australia’s most remarkable natural gift with more than 3000 coral reefs covering an area of 348,000 km2. The GBR contains a huge and marvellous natural habitat for different organisms and plays a critical role in conservation of biological diversity. Besides its environmental aspects, this wonder of nature has a substantial contribution to Australian economy as well. Despite the economic and environmental importance of the GBR, a number of menaces have recently emerged that potentially threaten the future of this beautiful testament. Elevated levels of sediments and nutrients discharged from adjacent coastal river systems have been considered as one of the main threats to the ecosystems of the GBR. While research has been mainly focused on the impact of agricultural activities on dissolved inorganic nitrogen (N) load of rivers in the GBR catchment, the origin and the fate of organic nutrients in both terrestrial and marine environments are not well understood. The overall purpose of this study was to provide insights into the key biogeochemical processes governing the movement and dynamics of soil, sediment and associated particulate organic nutrients in both terrestrial and marine ecosystems, and to improve our understanding of the main origin and fate of sediment and organic nutrients in the GBR catchment.