Loading of NPS pollutant was valued through simulation by using BASINS/HSPF model which can simulate runoff volume in rainfall by time. For the verification of the model, it was analyzed the scatter diagram of the simulation value and measure value of water quality and runoff volume in Dongcheon estuary. Using the built model, a study on the time-variant characteristics of runoff and water quality was simulated by being classified into four cases. The result showed the simulation value was nearly same as that of the measured runoff. In the result of fit level test for measured value and simulated value, correlation of runoff volume was computed high by average 0.86 and in the water quality items, fit level of simulation and measurements was high by BOD 0.82, T-N 0.85 and T-P 0.79.