The effort to manage diffuse pollution at the catchment scale is an ongoing challenge that needs to take into account trade-offs between environmental and economic objectives. Best Management Practices (BMPs) are gaining ground as a means to address the problem, but their application (and impact) is highly dependant on the characteristics of the crops and of the land in which they are to be applied. In this paper, we demonstrate a new methodology and associated decision support tool that suggests the optimal location for placing BMPs to minimise diffuse surface water pollution at the catchment scale, by determining the trade-off among economic and multiple environmental objectives. The decision support tool consists of a non-point source (NPS) pollution estimator, the SWAT (Soil and Water Assessment Tool) model, a genetic algorithm (GA), which serves as the optimisation engine for the selection and placement of BMPs across the agricultural land of the catchment, and of an empirical economic function for the estimation of the mean annual cost of BMP implementation. In the proposed decision support tool, SWAT was run a number of times equal to the number of tested BMPs, to predict nitrates nitrogen (N-NO3) and total phosphorus (TP) losses from all the agricultural Hydrologic Response Units (HRUs) and possible BMPs implemented on them. The results were then saved in a database which was subsequently used for the optimisation process. Fifty different BMPs, including sole or combined changes in livestock, crop, soil and nutrient application management in alfalfa, corn and pastureland fields, were evaluated in the reported application of the tool in a catchment in Greece, by solving a three-objective optimisation process (cost, TP and N-NO3). The relevant two-dimensional trade-off curves of cost-TP, cost-N-NO3 and N-NO3-TP are presented and discussed. The strictest environmental target, expressed as a 45% reduction of TP at the catchment outlet, which also resulted in a 25% reduction of the annual N-NO3 yield was met at an affordable annual cost of 25 @?/person by establishing an optimal combination of BMPs. The methodology could be used to assist in a more cost-effective implementation of environmental legislation.