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For lowering sediment, nitrogen (N) and phosphorus (P) pollution of surface water bodies at the catchment scale, environmental legislation require programs of pollution abatement measures. To be able to ensure the cost-effectiveness of such programs we first need to identify high risk areas, which give rise to increased pollutant runoff. Process-based GIS models provide the opportunity to identify such critical areas and hence better target diffuse pollution abatement actions. However, these models are data intensive and their spatially-distributed parameterization in poorly monitored catchments is not feasible without extensive input data pre-processing and significant simplifying assumptions. This study implements the widely-used SWAT river basin model (Soil Water Assessment Tool) to study a medium-sized Greek catchment with the typical data limitations met at the national level, in order to identify critical …