To quantify pollutant inflow load in wet weather and elucidate its influence on water and benthic quality in urban rivers, field surveys and laboratory experiment were conducted. As a result, water qualities of drainage water from the CSO outlets and freeway outfalls showed significant fluctuations according to precipitation variation. The pollutant inflow load in wet weather had a minor impact on the mass balance in the waters. Moreover, the results of stable isotope ratio analysis indicated that the organic matter from CSO outlets and freeway outfalls did not constitute a large portion of sediments in the rivers.