We explained the methodology used in setting the basic and supplementary measures for diffuse pollutants at Küçük Menderes Basin. As the majority of diffuse pollutants arise from livestock breeding and agricultural activities, we focused to propose measures regarded with tackling the pollution from agricultural activities. The types and distribution of diffuse loads were expressed by total nitrogen and phosphorous parameters. We used the results of a yearlong surface water quality monitoring involving physico-chemical, chemical and biological parameters with specific pollutants and priority substances,set in the European Union Water Framework Directive as the AquaTool input data. The AquaTool model was run for attaining the outcomes of a series of measures determined according to the ecological sensitivity of each water body. The removal efficiency of pollution loads provided by the best management practices in agricultural activities and livestock breeding were compiled from literature,and typical removal rates were further determined for the basin. We produced nine alternative scenarios at first cycle for determining compliance measures for mitigating point and diffuse sources of pollution in surface water bodies, and water quality improvements observed in the Model were reported. A number of exemptions were defined for some of the water bodies that could not achieve the environmental objectives at the end of first implementation cycle. 759 proposed measures for tackling diffuse pollution were 81% of the total measures considered. Additionally, the measures for mitigating diffuse agricultural pollution were almost equal to half of the diffuse pollutant measures, and 40% of the overall measures listed