Investigation and analysis of pollution sources and calculation of the amount of pollutants discharged into rivers are the important and basic issues for water environment protection. In this paper, with the characteristics of pollution yield in an economically developed complex river network region as an example, the mechanism of the point source pollution, area source pollution, and inner source pollution is studied in detail, and a method for investigation and estimation of the amount of pollutants discharged into rivers from each kind of pollution sources is discussed. The method is applied to the investigation of pollution sources and calculation of the amount of pollutants discharged into rivers of Zhangjiagang City, providing a basis for water environment planning and regulation for the city.