The management of fine sediment loads delivered to the Great Barrier Reef (GBR) is one of the fundamental priorities of the Reef 2050 Water Quality Improvement Plan. However, the knowledge of the key sediment that threaten the ecosystem first need to be defined, then sediment budgets of those sediments can be developed within higher spatial resolution. Here we provide a catchment to reef framework to identify and manage fine sediments from the Burdekin River basin. The Burdekin River contributes the highest anthropogenic load of fine sediments exported to the GBR and we highlight the particular importance of the <20 µm grain size fraction that is transported furthest in the marine ecosystem and is linked to suppressed water clarity over a prolonged period. We then show that the Bowen-Broken-Bogie (BBB) area that covers 10% of the vast 130,000 km2 Burdekin catchment area contributes ~60% of this < 20 µm grainsize loads. We then adopted a novel approach to integrate three independently derived sediment budgets produced from a catchment scale sediment budget model (Dynamic SedNet), targeted tributary water quality monitoring and geochemical sediment source tracing to refine and map the sediment source zones within the BBB area. The integrated sediment budget provides much higher confidence to managers to prioritise investment in the BBB area where major works in catchment remediation have commenced. An added benefit of this work was the strong collaboration forged between our project, NQ Dry Tropics Landholders Driving Change and importantly landholders within the BBB which has led to improved characterisation of sediments within this area and enhanced local understanding of catchment to reef water quality connections.