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Urban rivers are often characterized by high nitrate (NO3-) loadings. High NO3- loadings cause water quality and ecological damages, which undermines the sustainable development of cities. To date, the drivers of these high NO3- loadings remain unclear. This study, for the first time, integrated natural-abundance isotopes (delta15N/delta18O-NO3- and deltaD/delta18O-H2O) and 15N-pairing techniques to comprehensively reveal the anthropogenic impacts on the NO3- pollution in an urban river. Natural-abundance isotopes suggested that in both the wet and dry seasons, the NO3- was predominantly from the conservative mixing of different sources, and biological NO3- removal was minor. The 15N-pairing experiments supported the natural-abundance isotope data, quantitatively showing that in-soil nitrification was prevailing, while NO3- removal processes (denitrification, anammox, and dissimilatory NO3- reduction to ammonium) were weak. A Bayesian isotope-mixing model showed that soil sources (soil organic nitrogen and chemical fertilizer) dominated the NO3- in the upper reaches, while in the lower reaches, the impermeable riparian zone short-circuited the access of soils to the river. Here, the wastewater treatment plants became a significant source of NO3-. This study quantitatively revealed the drivers of high NO3- loadings in an urban river, and generated important clues for effective NO3- pollution control and remediation in urban rivers.