The effect of quality of irrigation water on the overall quality of surface water bodies has raised significant concerns in Taiwan. In this study, quantity and quality of water bodies of Meilon and Hunai Townships was simulated with the system dynamic simulation software, Vensim��, to investigate the interaction between polluted irrigation water and other water bodies and farm land. The water bodies analyzed included the return flow, streams, and groundwater. Four scenarios were selected for simulation in order to evaluate possible schemes to reduce the pollution loading in the return flow and, thus, the streams. These scenarios are: “deep-impounding irrigation”, “irrigation and discharge separation”, “farm fallow”, and “crop rotation”.