In this study we investigated the water quality of surface runoff and groundwater runoff from the basins of the Yodo River and the Asahi River based on that separated by a numerical filter. The water quality of the surface runoff is greatly different from the groundwater runoff. The tendency of concentration change in accordance with river discharges is different from each other. The water qtiality of groundwater runoff changes with river discharges clockwise in many cases. The differences of COD and SS originating from those of population and industrial activities in each basin are found in the lower SS concentrations of the surface runoff and the COD cencentrations of the groundwater runoff. The nutrients and chlorine ion were investigated, too.