A water quality model was developed for small stream at a upland agricultural watershed. A control volume method was employed to digest the severe variability of stream shape, water quality and discharge at small streams. We estimated optimum reaction coefficients and model structure using a random number generation technique. The index of agreement and coefficient of efficiency were introduced for the model calibration criterion. As the result, the reliability of model parameter estimation could be improved. The applicability of model was tested by a set of sampling results at Yongduckchun in Kimhae. The variability of water quality reaction coefficient was explored through the observed data and using the developed model. model.