Best management practices (BMPs) are an effective way to control water pollution. However, identification of the optimal distribution and cost-effect of BMPs provides a great challenge for watershed policy makers. In this paper, a semi-distributed, low-data, and robust watershed model, the Revised Generalized Watershed Loading Function (RGWLF), is improved by adding the pollutant attenuation process in the river channel and a bank filter strips reduction function. Three types of pollution control measures—point source wastewater treatment, bank filter strips, and converting farmland to forest—are considered, and the cost of each measure is determined. Furthermore, the RGWLF watershed model is coupled with a widely recognized multi-objective optimization algorithm, the non-dominated sorting genetic algorithm II (NSGAII), the combination of which is applied in the Luanhe watershed to search for spatial BMPs for dissolved nitrogen (DisN). Fifty scenarios were finally selected from numerous possibilities and the results indicate that, at a minimum cost of 9.09 × 107 yuan, the DisN load is 3.1 × 107 kg and, at a maximum cost of 1.77 × 108 yuan, the total dissolved nitrogen load is 1.31 × 107 kg; with the no-measures scenario, the DisN load is 4.05 × 107 kg. This BMP optimization model system could assist decision-makers in determining a scientifically comprehensive plan to realize cost-effective goals for the watershed.