Water quality simulation models include the difference between the measured and estimated values as an inevitable consequence because they represent the complicated natural phenomena as simplified mathematical equations. The major reason of the difference occurrence is due to the use of the imprecise values of the model parameters, but the parameter values are currently determined by the try and error method directly performed by humans. However, the use of this method requires many time and endeavor of humans, and generally does not obtain the most suitable parameter values. A method for deciding model parameter values is, therefore, developed in this study. The method minimizes the difference between the measured and estimated values and also distributes uniformly the measured values on the upper and lower sides of the line representing the estimated values. A user interface based on this method is also developed by using the Visual Basic 6.0 of Microsoft, and it can be operated in the environment of Windows 98/2000. In this study, the method for deciding model parameter values is applied for estimating the water quality of the stream Ko-heung. The results of the application show that the method, including its computer program, can effectively obtain the most suitable parameter values and also save many working time in comparison with the existing method directly performed by humans.