Water resources are a vital element and main issue for the development of southwest Taiwan. This paper concludes that the distribution of pig farms, human population and industries has a significant impact on water quality. The data shows that a reduction of pig population can reduce stream pollution and improve water quality. In this research, the RPI data shows that water quality in up stream area is getting better while the down stream section, including the tributaries, is getting worse. Besides, there is also some difference between the high and low water level period. Generally speaking, the RPI is lower during the high water level period because of dilution. But there are 5 stations that do not show this trend because of the increase in suspended solids during the high water level period. In water quality, the study shows obvious difference between up and down stream sections. WQI in up stream areas is over 50 and it is getting better while it is lower than 40 and getting worse in the nearby tributaries of the down stream section. It is mainly affected by the output of pig farming. The WQI is about 50 to 60 at the Kao-Ping Bridge and Shuan-Yuan Bridge stations because of higher discharge. Moreover, there is some difference between high and low water level periods. Generally speaking, the WQI is higher during high water level periods because of dilution. Only two stations do not show this trend due to the increase of suspended solids in higher discharge.