The characteristics of nitrate (NO₃⁻) in major rivers and aquifers of the Sanjiang Plain, China were investigated by hydrogeochemical conditions, nitrogen isotope technique and CFCs trace. An overall understanding on the sources and fate of NO₃⁻ in the surface water and the groundwater was obtained. The NO₃⁻ concentrations in the surface water were low and no samples exceeds the WTO standards. However, 11.4% of the groundwater samples exceeded the WTO standards, indicating local NO₃⁻ pollution in rural areas. Redox condition analysis revealed that most of the surface water had oxic condition, while for the shallow groundwater (mean well depth smaller than 30 m), the redox condition began to change into anoxic zone, and the deep groundwater (mean well depth larger than 50 m) showed strong anoxic condition. The δ¹⁵N-NO₃ data indicated soil N and fertilizer contributed the major sources in the surface water, and NO₃⁻ in the groundwater mainly showed a manure origin. In the Songhua–Heilong River, dilution effect was dominating, while for the Wusuli River, it showed that mix with water contained excess of NO₃⁻ resulted in the NO₃⁻ concentration increased along the river. Additionally, the NO₃⁻ transportation in the groundwater was analyzed by groundwater ages derived from environmental tracer (CFCs) data. The relation between the groundwater ages and the NO₃⁻ concentrations showed that the young groundwater with the age less than 60 years had higher NO₃⁻ concentrations than the old groundwater over the age of 60 years because anthropogenic activities began to boom from 1950s in the Sanjiang Plain.