Dual isotopes of nitrate (¹⁵N and ¹⁸O) and carbon isotopes of dissolved inorganic carbon (¹³C) together with water chemistry were used to identify the sources and fate of nitrate in the upper stream of Chaobai River, north China. The results show that NO₃⁻ concentrations ranges from 0.03 mmol L⁻¹ to 0.80 mmol L⁻¹. Sampling sites from watershed with dominant forest land had higher NO₃⁻ concentrations and lower δ¹⁵N–NO₃⁻ (<10‰) in the wet season than in the dry season, while those from watershed with more anthropogenic activities had lower NO₃⁻ concentrations and higher δ¹⁵N–NO₃⁻ (>10‰) in the wet season. Compositions of isotopes and chemistry indicated that NO₃⁻ originated mainly from soil N, sewage and livestock wastes and atmospheric nitrogen. Furthermore, the mixing model suggested that soil N was the major NO₃⁻ source in the wet season, while the sewage and livestock wastes contributed the most in the dry season. Compared to rivers, the Miyun Reservoir had a higher contribution of atmospheric N and the N input from the upper rivers exerted significant influence over the reservoir. Mineralization and nitrification played an important role in N biogeochemistry based on the isotopes (¹⁵N and ¹⁸O and ¹³C) and chemical data. There appeared to be no significant denitrification in the watershed according to the three isotopes and chemical ions. The combined use of ¹⁵N, ¹⁸O and ¹³C proved to be useful for further identification of the sources and fate of nitrate in watersheds with dominant forest land in the wet season.