Abstract: With the control of point source pollution, the agricultural non-point source pollution is becoming the major factor affecting water quality. In Ningxia Yellow River irrigation region, one of China’s important commodity grain production areas, high-input in agriculture exacerbates the local water quality. This article analyzed water quality of the Yellow River flowing over several monitoring sections and of main drainage ditches in Ningxia. The results show that water quality of the Yellow River in Ningxia is mainly affected by agricultural irrigation return flow, industrial wastewater and domestic sewage. The water quality becomes worse after flowing through Ningxia with one class decreasing of comprehensive pollution index illustrating a certain degree of pollution. The main pollutants in Ningxia Yellow River irrigation region are Ar-OH, NH₄⁺-N, COD_Mn and BOD₅, which are decreasing generally from 2002 to 2007 in company with the reducing comprehensive pollution index. Water quality of main drainage ditches of the region is inferior class Ⅴ with 100% overproof monitoring sections. Its main pollutants are NH₄⁺-N, COD_Cr, BOD₅. The analysis on non-point pollution source shows that TN and NH₄⁺-N mainly come from farming, followed by breeding industry and the Yellow River water. Farming and livestock breeding are the main resources of TP. Most COD is from livestock breeding. The large amount of pollutants in farmland irrigation return flow is one of the major factors leading to deterioration of water quality in Ningxia.