Non-point sources of water pollution caused by agricultural crop production are a serious problem in Czechia, at present. This paper describes a new approach for the mutual delineation and assessment of different pollution sources where the critical points method is used to identify the origin of contamination and the source areas. The critical points, i.e., sites presenting the entry of quick surface and drainage runoff into waters, are classified into three (for surface pollution sources using a WaTEM/SEDEM model) or four (subsurface = drainage sources via the catchment-measures need index) categories, respectively. This enabled us to prioritize the most endangered areas at different scales, ranging from the third-order catchments to very small subcatchments, and to design the appropriate combination of control measures to mitigate surface and drainage water runoff, with these being the main drivers of associated pollution. This methodology was applied to a study conducted in the Czech Republic within the entire Vltava River basin, with a total area of 27,578 km2, and utilized in depth to assess a 543 km2 catchment of the Vlašimská Blanice River. When the effect of the designed surface runoff control measures system had been assessed for sediment transport through outlet profiles of the fourth-order catchments, the average reduction reached 43%. The total reduction in the subsurface transport of nitrogen within the fourth-order catchments was 24%. The approach and results are planned to be projected into river basin management plans for the Vltava River basin. Nevertheless, a thorough reassessment of current legislations and strategies is needed to enable the broader adoption of mitigation measures and sustainable management patterns within agricultural landscapes.