Water quality remains a main reason for the failure of waterbodies to reach Good Ecological Status (GES) under the European Union Water Framework Directive (WFD), with phosphorus (P) pollution being a major cause of water quality failures. Reducing P pollution risk in agricultural catchments is challenging due to the complexity of biophysical drivers along the source-mobilisation-delivery-impact continuum. While there is a need for place-specific interventions, the evidence supporting the likely effectiveness of mitigation measures and their spatial targeting is uncertain. We developed a decision-support tool using a Bayesian Belief Network that facilitates system-level thinking about P pollution and brings together academic and stakeholder communities to co-construct a model appropriate to the region of interest. The expert-based causal model simulates the probability of soluble reactive phosphorus (SRP) concentration falling into the WFD high/good or moderate/poor status classifications along with the effectiveness of three mitigation measures including buffer strips, fertiliser input reduction and septic tank management. In addition, critical source areas of pollution are simulated on 100 × 100 m raster grids for seven catchments (12–134 km2) representative of the hydroclimatic and land use intensity gradients in Scotland. Sensitivity analysis revealed the importance of fertiliser inputs, soil Morgan P, eroded SRP delivery rate, presence/absence of artificial drainage and soil erosion for SRP losses from diffuse sources, while the presence/absence of septic tanks, farmyards and the design size of sewage treatment works were influential variables related to point sources. Model validation confirmed plausible model performance as a “fit for purpose” decision support tool. When compared to observed water quality data, the expert-based causal model simulated a plausible probability of GES, with some differences between study catchments. Reducing fertiliser inputs below optimal agronomic levels increased the probability of GES by 5%, while management of septic tanks increased the probability of GES by 8%. Conversely, implementation of riparian buffers did not have an observable effect on the probability of GES at the catchment outlet. The main benefit of the approach was the ability to integrate diverse, and often sparse, information; account for uncertainty and easily integrate new data and knowledge.