The Hsintien Stream is one of the major branches of the Danshuei River system, which runs through the metropolitan capital city of Taipei, Taiwan and receives a large amount of wastewater. The dissolved oxygen concentration is generally low in the tidal portion of the Hsintien Stream. Hypoxia/anoxia occurs often, particularly during the low-flow period when the Feitsui Reservoir, Chingtan Dam and Chihtan Dam impound the freshwater for municipal water supply. Fish kills happen from time to time. This paper describes the application of a numerical hydrodynamic and water quality model to the Danshuei River system, with special attention to the tidal portion of the Hsintien Stream. The model is recalibrated with the prototype conditions of the year 2000. The hydrodynamic portion of the model is recalibrated with measured surface elevation and velocity at various stations in the river system. The water quality portion of the model is recalibrated with respect to the field data provided by Taiwan EPA. The input data of point and nonpoint sources are also estimated. The model simulates the concentrations of various forms of nutrients, CBOD and dissolved oxygen. A series of sensitivity runs was conducted to investigate the effects of point source loadings and river flow on the DO level in the river. It is demonstrated that the augmentation of river flow has as much effect on raising DO level as the reduction of point source loadings. The completion of the Taipei sewer project is expected to reduce the point source loadings by at least 75%. Under these reduced loadings, if the daily instream flow is maintained above the monthly Q75 flow throughout the year, the minimum DO concentration in the river would not fall below 1mg/L, which is the suffocation level for most fish species in the Hsintien Stream. (Q75 is the flow which is equaled or exceeded 75% of the days in the month.) The Feitsui Reservoir, Chingtan Dam and Chihtan Dam may impound water during the high flow periods and release freshwater to maintain the flow at the Q75 value in the Hsintien Stream during the drought periods.