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The Beiyun river flows through a hot spot region of Beijing-Tianjin-Hebei in China that serves a majority of occupants. However, the region experiences severe nitrate pollution, posing a threat to human health due to inadequate self-purification capacity. In that context, there is an urgent need to assess nitrate levels in this region. Herein, we used δ15N-NO3, δ18O-NO3 isotopes analysis, and stable isotope analysis model to evaluate the nitrate source apportionment in the Beiyun river. A meta-analysis was then used to compare the potential similarity of nitrate sources among the Beiyun riverine watershed and other watersheds. Results of nitrate source apportionment revealed that nitrate originated from the manure & sewage (contribution rate: 89.6%), soil nitrogen (5.9%), and nitrogen fertilizer (3.9%) in the wet season. While in the dry season, nitrate mainly originated from manure & sewage (91.6%). Further, different land-use types exhibited distinct nitrate compositions. Nitrate in urban and suburban areas mostly was traced from manure & sewage (90.5% and 78.8%, respectively). Notably, the different nitrate contribution in the rural-urban fringe and plant-covered areas were manure & sewage (44.3% and 32.8%), soil nitrogen (26.9% and 35.7%), nitrogen fertilizer (23.5% and 29.4%), and atmospheric deposition (5.3% and 2.0%). Through a meta-analysis, we found nitrogen fertilizer, soil nitrogen, and manure & sewage as the main nitrate sources in the Beiyun riverine watershed or the other similar complex watersheds in the temperate. Thus, this study provides a scientific basis for nitrate source apportionment and nitrate preventive management in watersheds with complex land-use types in temperate regions.