This study utilizes the river and stream water quality (QUAL2K) model as a tool to simulate and forecast the water quality and then to develop the management strategies for various flow rates above the Kaoping weir of Kaoping River in Taiwan. Model results based on the river assimilative capacity of four various flow rates including Q95, Q75, Q60, and Q25 were conducted to determine the corresponding amounts of pollution reduction. The average pollution reduction ratios of biochemical oxygen demand (BOD5) and ammonia nitrogen (NH3-N) should at least reach to 42.0% and 28.3% respectively to meet the restoration goals of Class A water quality standards regulated by Taiwan. The modeling results demonstrate that an increase of water extraction rates in the upstream reaches will have significant adverse effects on the water quality of the Kaoping River. Higher water extraction rates will lower the assimilative capacity that reduces the buffering capacity of river. It also induces that the water quality is susceptible to the impacts of the influent pollutant loads from the tributaries or drainages.