The Australian Government's Coastal Catchment Initiative (CCI) seeks to achieve targeted reductions in nutrient pollution to key coastal water quality hotspots, reducing algal blooms and fish kills. Under the CCI a Water Quality Improvement Plan (WQIP) is being prepared for targeted estuaries (Swan-Canning, near Perth, and the Vasse-Geographe, 140 km south of Perth) to address nutrient pollution issues. A range of projects are developing, testing and implementing agricultural Best Management Practices (BMPs) to reduce excessive loads of nutrients reaching the receiving waters. This work builds on progress-to-date achieved in a similar project in the Peel-Harvey Catchment (70 km south of Perth). It deals with the necessary steps of identifying the applicability of BMPs for nutrient attenuation, developing and promoting BMPs in the context of nutrient use and attenuation on farm and through catchments and estimating the degree to which BMP implementation can protect receiving waters. With a range of BMPs available with varying costs and effectiveness, a Decision Support System (DSS) to guide development of the WQIP and implementation of BMPs to protect receiving waters, is under development. As new information becomes available the DSS will be updated to ensure relevance and accuracy for decision-making and planning purposes. The DSS, calibrated for application in the catchments, will play a critical role in adaptive implementation of the WQIP by assessing the effect of land use change and management interventions on pollutant load generation and by providing a tool to guide priority setting and investment planning to achieve agreed WQIP load targets.