The monthly natural runoff of Nanfeihe River System in 2017 and 2018 was analyzed. The pollution fluxes into Chaohu Lake in each month in 2017 and 2018 were calculated according to the volume of water and the major pollutants into the river from wastewater treatment plants. The pollution fluxes were analyzed and the idea of harnessing the Nanfeihe River was proposed. The historical problems of direct and mixed sewage discharge in urban areas should be solved. More attention should be paid to the initial rainwater in urban built-up areas and the blind spots of rural non-point source pollution. Its suggested to ease the lack of river base flow and the unsmooth the problem of river channel. The integrated treatment model of urban heavily polluted river should be adopted.