Optimization methods usually obtain the travel direction of the solution by substituting the solutions into the objective function. However, if the solution space is too large, this search method may be time consuming. In order to address this problem, this study incorporated the Taguchi method into the solution space search process of the optimization method, and used the characteristics of the Taguchi method to sequence the effects of the variation of decision variables on the system. Based on the level of effect, this study determined the impact factor of decision variables and the optimal solution for the model. The integration of the Taguchi method and the solution optimization method successfully obtained the optimal solution of the optimization problem, while significantly reducing the solution computing time and enhancing the river water quality. The results suggested that the basin with the greatest water quality improvement effectiveness is the Dahan River. Under the optimal strategy of this study, the severe pollution length was reduced from 18 km to 5 km.