We study the basic theory and applicability of the WQUAL block in the FFC2Q model and the characteristics of non-point pollutant loads during the early stage of runoff. Study is also performed on selection of the values of the related parameters and their effect on the simulation results. FFC2Q simulation results are compared for verification with the measured data for three rainfall events in the Gunja Subbasin and found to be similar to the measured data in peak-flows, total runoff volumes, total loads, peak concentrations and times of peak concentration. This model thus shows results very close to those applying the SWMM and MOUSE models, even though it uses simplified input data. Related to rainfall distribution, under the condition of Huff 1st quartile distribution the pollutant loads occurred earlier than under other conditions, and in the early stage of rainfall the BOD and COD loads increased faster than the SS loads. The NPS loads were concentrated in the early stage of rainfall and finally reached total loads, so the rainfall after that could not contribute so much to the NPS loads.