The Paddock to Reef Modelling (P2R) and Monitoring Program reports on progress towards meeting the Reef Water Quality Protection Plan (Reef Plan) targets. The targets set out in the Reef Plan are designed to improve water quality entering the Great Barrier Reef (GBR) through improving land management practices. Catchment modelling is being used as one line of evidence to report on progress towards Reef Plan targets resulting from investment in improved management practices. The eWater Source Integrated Modelling System (Source IMS) was chosen as the preferred modelling platform for undertaking GBR water quality modelling. The main reason for choosing eWater source was its flexible architecture that enables users to write customised plug-ins to meet specific modelling requirements. After a review of currently available modelling platforms, it was determined that there was no "off the shelf" software that could meet all of the modelling requirements. SedNet alone could not provide the finer resolution time stepping required, and Source IMS cannot inherently represent many variations of a spatially varying practice like cropping, to the level of detail required to allow subtle changes in management system to have a recognisable effect on model outputs. To address these issues, and answer the questions being posed by policy makers, customised plug-ins for Source IMS were developed. These plug-ins allowed us to integrate the best available data sources and landscape process understanding into the catchment model. Purpose built routines enabling representations of processes such as the effects of temporally and spatially variable ground cover on soil erosion, aggregation of deterministic crop model outputs directly into the catchment model and the incorporation of SedNet gully and stream bank erosion algorithms were developed. Additional reporting tools were also written to enable rapid interrogation of model outputs. For example, reporting of pollutant loads by subcatchment, landuse, process (gully, streambank, hillslope) for any time period from daily to average annual. The development of the GBR Source Catchments models demonstrates the highly flexible nature of the Source IMS framework. With flexibility also comes a tendency towards ever increasing complexity. As more involved questions are posed, it is tempting to keep adding to the functionality of the model. Although the modelling framework is capable of supporting complex algorithms it is essential that these are also supported by observed data and understanding derived from experimentation.