The purpose of this study is the prediction of pollutant loads into Seomjin river watershed using neural networks model. The pollutant loads into river watershed depend upon the water quantity of inflow from the upstream as well as the water quality of the inflow into the river. For the estimation of pollutants into river, a neural networks model which has the features of multi-layered structure and parallel multi-connections is used. The used water quality parameters are BOD, COD and SS into Seomjin river. The results of calibration are satisfactory, and proved the availability of a proposed neural networks model to estimate short-term water quality pollutants into river system.