It is considered that refractory dissolved organic substances have caused an increase in the COD concentration in Lake Biwa in recent years. We investigated the organic matter in the first flush of stormwater runoff from a road in the watershed area of the lake, and studied the possibility of improvement in the water environment from that aspect. After percolating the stormwater through soil, we analyzed organic substances fractionated by using GPC-TC. And we examined the effect of removal of organic substances by comparing the peak height before and after percolation. In the result of the experiments, we found that soil infiltration reduced the refractory dissolved organic substance and we successfully designed a system for a simple and easy experimental facility to treat urban runoff.