It is significant to design best management practices (BMPs) and determine the proper BMPs placement for the purpose that can not only satisfy the water quantity and water quality standard, but also lower the total cost of BMPs. The spatial rainfall variability can have much effect on its relative runoff and non-point source pollution (NPSP). Meantime, the optimal design and placement of BMPs would be different as well. The objective of this study was to discuss the relationship between the spatial variability of rainfall and the optimal BMPs placements. Three synthetic rainfall storms with varied spatial distributions, including uniform rainfall, downstream rainfall and upstream rainfall, were designed. WinVAST model was applied to predict runoff and NPSP. Additionally, detention pond and swale were selected for being structural BMPs. Scatter search was applied to find the optimal BMPs placement. The results show that mostly the total cost of BMPs is higher in downstream rainfall than in upstream rainfall or uniform rainfall. Moreover, the cost of detention pond is much higher than swale. Thus, even though detention pond has larger efficiency for lowering peak flow and pollutant exports, it is not always the determined set in each subbasin.