305 groundwater samples from wells in Miyun Reservoir watershed were collected from November to December, 2008, and nitrate nitrogen (NO3--N) concentrations in groundwater were tested. Average NO3--N concentration for all wells sampled was 6.81mg/L, and 16.07% of all wells exceeded 10mg/L, the WHO limit for NO3--N in drinking water. Among them, 35 wells from villages and 13 wells from vegetable lands show high NO3--N concentrations with averages of 9.52 mg/L and 9.55mg/L respectively, near the WHO limit. 28.57% of village wells and 23.07% of vegetable land wells respectively exceeded the WHO limit. 219 wells from croplands (corn and soybean) presented the middle NO3--N concentrations with average of 6.59mg/L and of which 16.08% were above the WHO limit. 10 wells from woodlands demonstrated low NO3--N concentrations with average of 2.66mg/L and none of them were beyond the WHO limit. Nitrate pollution of groundwater in Chaohe River basin was more severe than that in Baihe River basin. Average NO3--N concentration in groundwater from farmlands in Chaohe River basin reached 8.42mg/L, which was higher than that (5.03mg/L) in Baihe River basin. 25% of 124 wells from farmlands exceeded the WHO limit in Chaohe River basin while only 6.56% of 122 wells did in Baihe River basin. High nitrate concentrations in groundwater resulted from more intensive agriculture in Chaohe River basin. NO3--N concentrations in groundwater from farmlands along the rivers increased from upstream to downstream. NO3--N concentrations in groundwater from corn fields decreased toward the rivers, related negatively with groundwater tables and positively with nitrogen fertilizer applications. There might be potential risks for NO3--N concentrations exceeding the WHO limit as groundwater tables are lower than 7 meters or annual fertilizer applications are more than 200kgN /hm2 in corn fields.