Agricultural production is considered one of the most important sources of water quality deterioration in the Taihu Lake Basin, China. Crop farming, livestock & poultry breeding and aquaculture are primary agricultural non-point sources and their impacts on the water environment are, in most cases, evaluated separately. Therefore, it is a challenge for current research to consider all of the different agricultural non-point sources as a whole and assess their combined influence on the water environment. The purpose of this paper is to evaluate the conjoint impact that agricultural non-point sources such as crop farming, livestock & poultry breeding and aquaculture have had on the local water environment in the Taihu Lake Basin by taking Huzhou City of Zhejiang Province as a case study. To achieve this, a new, innovative approach named the “Waste Absorption Footprint” (WAF) is applied. The results show that nitrogen and phosphorus pollution generated by agricultural production are more serious than that of organic substances, while aquaculture and crop farming are more critical pollution sources compared with livestock and poultry breeding, and so they should be the focus of environmental management and pollution control initiatives. There is a regional discrepancy in the spatial distribution of agricultural non-point source pollution across counties and districts, which provides information for determining the key regions for the treatment of agricultural pollution. This study demonstrates that the WAF method can make a comprehensive assessment of the influence of agricultural production on the water environment and provide references for the control and management of agricultural non-point source pollution, which is of great importance for management of the water environment.