Single factor water quality identification index was adopted to assess the surface water quality of Miyun reservoir watershed in Beijing using nearly 20 years monitoring data of 4 sites, also the surface water quality pollution sources were analyzed. The results indicated TP had the largest temporal variation at every monitoring site, coefficients of variation were 93.86%, 86.08%, 50.56% and 139.47%, respectively. The following element was Hg, the coefficients of its variation were 86.08%, 25.75%, 56.52% and 47.01%, respectively. While TN, permanganate index, BOD5, Pb and Cr were relatively stable with small coefficient of temporal variation. The permanganate index, BOD5, Pb and Cr did not exceed to the Chinese surface drinking water standard limit in the study period, while Hg had high pollution risk in several years, such as monitoring sites S1 and S3 in 1992, monitoring sites S4 in 1996. The major pollutants of Miyun reservoir watershed in Beijing were TN and TP, and TN had larger pollution risk compared with TP in most years. Comparing to that before the 1990s, the decade average fertilizer, pesticide and agricultural plastic mulch inputs after the 1990s had increased by 46%, 173% and 359%, respectively. The husbandry proportion in agriculture rose from 24.4% to 39.8%, and the average gross industrial production by 424%. The upstream of Miyun reservoir had larger pollution risk than its downstream. In addition, Chaohe watershed contributed more TN and TP to the reservoir than Baihe watershed.