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After analyzing the sources to pollute the Upper Yellow River in Ningxia and Inner Mongolia, we have found that Agriculture is becoming the most contributive pollution source in the area.Cropping system contributed 66% of total run-off nitrogen (TN) and 80% of NH4+ nitrogen, and animal fanning occupied 67% of total COD, and cropping system and animal farming respectively offered 45% and 54% of total washed phosphorus in fiver-irrigated area in Ningxia in 2007.While the pollutants of TN and COD from industries and daily life in urban area was respectively only 1% and 14% in Ningxia in the same year.In Inner Mongolia, the total TN and COD from rural areas was approximately 70% and 45% separately.