The contradiction between ecological environment protection and economic development in the Yangtze River Basin has become increasingly prominent in recent years, which seriously limits the sustainable development of the basin. Research on water environment changes of the main tributaries of the Yangtze River helps explore measures to improve the ecological environment of the Yangtze River Basin. In this study, based on the theory of behavioral science in modern management, water quality data in the field were collected, and the farmers’ garbage stacking behavior was also investigated in the water source area of the Dabie Mountains. The results showed that ammonia nitrogen (AN), chemical oxygen demand (COD), total organic carbon (TOC), and total dissolved solids (TDS) in the water bodies showed an overall negative correlation with the distance of water quality collection sites from the garbage stacking point. AN was the most important pollution element affecting the rural water quality in the water source area of the Dabie Mountains. The unsuitable garbage stacking locations and the farmers’ behavior of dumping garbage along the riverbanks were the important causes of water pollution. The garbage stacking locations were optimized and designed by using a GIS spatial analysis tool and a developed suitability evaluation model for the garbage stacking points. The optimized garbage stacking locations were more suitable for improving the local water environment, and their average suitability values increased to 2.01 times and 2.94 times that of the original stacking locations in Kanxiawan and Lengshuigou, respectively. This study can be used as a scientific and methodological reference for improving the rural water environment in the water source area of the Dabie Mountains and in other similar regions in the world.