Great Barrier Reef (GBR) catchments have been extensively modified over the past 150 years for agricultural production, leading to a decline in water quality entering the GBR lagoon. A joint Queensland and Australian government initiative produced the Reef Water Quality Protection Plan (Reef Plan) in 2003 in response to the decline in water quality, updating the plan in 2009 and most recently in 2013. The Reef Plan outlines a clear set of water quality and management practice targets for sediment, nutrients and pesticides. Improvement in water quality is achieved through government and landholder investment into improved agricultural management practices. A Paddock to Reef Integrated Monitoring and Modelling, Reporting program (Paddock to Reef) has been established to measure and report progress towards meeting Reef Plan goals and targets, and to assess the benefits of improved land management practices on water quality discharged to the reef lagoon. The program integrates five lines of evidence including: monitoring of practice effectiveness, prevalence of adoption of improved practices and catchment indicators through time, paddock and catchment modelling, and catchment and marine monitoring and remote sensing. Paddock to Reef is an innovative program where paddock and catchment modelling is an essential component used to report on progress towards meeting reef water quality targets. An important innovation is the linking from paddock through to catchment scale models to assess the impact of changes in management practices on end of system loads