With the effective control of point source (PS) pollution accomplished, water pollution problems caused by non-point source (NPS) pollution have increased in recent years. The worsening agricultural NPS pollution has drawn the attention of the Chinese Government and researcher scientists and has resulted in the often mentioned "three red lines" on water resources management. One of the red lines is to control water pollution within a rational range. The Agricultural NPS pollution, which includes pollution from housing, and from livestock and crop production, is the main source. Based on the NPS pollution statutes, an index system for integrated evaluation of water quality, and a zoning scheme for rural water conservation were established. Using the method of one-dimensional Euclidean distance, this country is divided into 9 sub-zones at the provincial level, which are the first level zones. The zoning themes include natural resources, socio-economic development, water use efficiency, and pollutants emission intensity. According to pollution types of livestock, agriculture, or both, the first level zones are divided into 25 second level zones. The third class zoning is divided also based on pollution intensity of total nitrogen (TN), total phosphorus (TP), ammonia nitrogen (NH 3 -N), chemical oxygen demand (COD), and biochemical oxygen demand (BOD). On the basis of the second level zoning, there were formed 70 rural water conservation third level zones. This case study in the Ashihe river watershed indicated that the main pollution sources are consistent with the zoning research result, and this zoning has shown a good way to guide the agricultural NPS pollution control in not only the wide rural area of China but also other parts of the world.