The single factor pollution index method and Nemerow index method were used to analyze the status of water quality and its trend at the Zhangwan and Shendinghekou cross-sections through the tributaies flowing into the Danjiangkou Reservoir during the period from 2005 to 2014. The results show that the Zhangwan cross-section was heavily polluted during the study period, and the main pollutants had been controlled to a certain extent. On the whole, the water quality of the Zhangwan cross-section has improved. The pollutants of the Shendinghekou cross-section always exceeded the standard significantly, and the water quality at this cross-section was below the grade V level from 2005 to 2014. Some pollution control measures should be taken to improve the water quality and enhance protection and management.