This paper presented the characteristics of nitrogen and phosphorus pollution in Beijing surface water during the survey. A significant difference was found out in concentration distribution of various parameters of nitrogen and phosphorus. Most water bodies in five water systems were polluted by total nitrogen with the content even up to 120 mg/L which was higher than exceeded the fifth class standard of national surface water quality standard GB3838-2002 except for several segments of Chaobaihe and Yongdinghe. Ammonia and phosphorus showed a similar tendency of distribution with higher content in Daqinghe, Beiyunhe and Jiyunhe water systems, but with relatively low concentrations in Chaobaihe and Yongdinghe water systems. Meanwhile, nitrate was found at comparatively low content(mostly less than 10 mg/L) and could fit for corresponding water quality requirements. Totally, the water quality of Daqinghe, Jiyunhe and Beiyunhe river systems as well as the lower reaches of Yongdinghe and Chaobaihe was contaminated seriously with high content of total nitrogen and phosphorus. Through multivariate statistical approaches, it can be concluded that total nitrogen, ammonia and total phosphorus was highly correlated to chemical oxygen demand, biochemical oxygen demand, dissolved oxygen and electrical conductivity, which explained the same pollution source from anthropogenic activities.