The Niulanjiang River-Dianchi Lake Water Supplement Project, as a synthetic utilization project of water resources in Dianchi Lake basin and surrounding areas, is crucial for increasing the ecological and environmental water supplement and improving the quality of water resources in Dianchi Lake. As a consequence, this project plays a great strategic role in ensuring the construction of the new Kunming city and the economic and social sustainable development of Yunnan Province. But the monitoring results of recent years suggest that the quality of water resources in the Niulanjiang River has entered in a downtrend. Non -point source pollution has been considered as the major pollution sources in previous studies. This research shows that the major pollutant in the Niulanjiang River is total phosphorus, which mainly comes from the industrial discharge, most being found at the Qixingqiao Section. And based on the research, this paper also proposed some water resources protection countermeasures to control the water pollution. The reliability of the conclusion has been proved by the result of water environment governance measures and water quality monitoring.