In the premise of consideration of age-longed development, it consists of very complicated and challengeable strategies to deal with managerial problem on river basin. This study is focus on the field of Tam Sui River. It is difficult to use numerical simulation in the following situation: The affect of tide on tidal river, the complication of hydrodynamic, and the formation of net-type Tam Sui River by three main confluents. The purpose of establishing hydrodynamic and water quality modeling with STELLA, a software used in systematic dynamic is to provide a valuation benchmark in water quality management. In water system, we want to understand the correlation and mechanism among parameters, and these will help us investigate and analyze the problems in water plan. We also want to make the best choice and decision and gain the biggest efficiency by understanding the characteristics and the contents of water quality. We use one dimension of movement equation in programming STELLA. And we solve hydrodynamuc in different time and different place by using¡unon-linear implicit finite-difference ¡v. In the result of our study, it can not completely simulate the whole situation of turbulence. But in the period of typhoon and flood, the prediction of water line is similar with the real survey in the complexit field. And the one-dimension model is easier to deal with and time-saver than 2-dimension model and 3-dimension model. In the aspect of water quality, we try to apply related mass balance equation in Water Quality Analysis Simulation Program (WASP) to find the chemical reaction among 8 parameters including chlorophyll A, organic phosphorus,inorganic phosphorus,organic nitrogen,ammonia,nitrate,carbonaceous biochemical oxygen demand,dissolved oxygen.After the test and verification, the simulation result meets our expectation and the theoretic value. This model could be extensively applied