Water quality is the key problem that water management departments concern. Water quality of Beijing segment of South-to-North Water Diversion Middle Route Project is closely related to water security and social stability in Beijing. Since the connection of Beijing part in Middle Route of South-to-North Diversion Project, water quality data of Daning regulation and storage reservoir and Daning surge tank was collected, and water quality indexes including water temperature, total nitrogen, nitrate nitrogen, chloride ion, sulfate, dissolved oxygen, permanganate index, pH, ammonia nitrogen, fluorine ion and total phosphorus, were monitored monthly. With variance analysis, water quality difference among different water sources of the South-to-North Water Diversion of Middle Route was analyzed. With factor analysis method, the water quality risk factors of Daning regulation and storage reservoir and Daning surge tank were identified. The results were as following, water from Hebei province had higher contents of nitrate nitrogen, total nitrogen, fluorine ion, chloride ion and sulfate than those of water from Danjiangkou reservoir, but the water quality was not as good as that from Danjiangkou reservoir. LSD difference test results showed that the dissolved oxygen, nitrate nitrogen and total nitrogen of the water from Hebei province had significant differences (P<0.05) between flood season and non-flood season, there was significant difference (P<0.05) in pH of water from Danjiangkou reservoir between flood season and non-flood season, and the water quality of Danjiangkou reservoir was more stable than water from Heibei province. No matter in flood season or non-flood season, there were no significant differences (P<0.05) in pH, dissolved oxygen, permanganate index, total phosphorus and ammonia nitrogen between the water from Danjiangkou reservoir and Heibei province, but there were significant differences (P<0.05) in nitrate nitrogen, total nitrogen, fluorine ion and sulfate ion and chloride ion. Contents of Nitrate nitrogen, total nitrogen, sulfate and chloride ion in 2015 (the mixture of water from Hebei province and Danjiangkou reservoir) in Daning regulation and storage reservoir were lower than those in 2012-2014 (water from Hebei province), and the water from Danjiangkou reservoir played a key role in dilution and adjustment of the water from Hebei province in Daning regulation and storage reservoir. The water quality differences test results between 2012-2014 and 2015 showed that there were significant differences (P<0.05) in the nitrate nitrogen, total nitrogen, fluorine ion, sulfate and chloride ion both in flood season and non-flood season, and the water quality of 2015 was better than that of 2012~2014 in non-flood season, but the differences of pH, dissolved oxygen, permanganate index, total phosphorus, ammonia nitrogen were not obvious (P<0.05). The difference test results between Daning regulation and storage reservoir and Daning surge tank showed that Permanganate index, total nitrogen, fluorine ion, sulfate and chloride ion had significant differences (P<0.05) both in flood season and non-flood season, and the contents of permanganate index, fluorine ion, sulfate and chloride ions in Daning regulation and storage reservoir were higher than those in Daning surge tank. The factor analysis results indicated that water quality potential risk factors both in Daning regulation and storage reservoir and Daning surge tank were mainly nitrogen, including ammonia nitrogen, nitrate nitrogen and total nitrogen, and potential risk factors also included total phosphorus in Daning regulation and storage reservoir.