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 (δ15 N/δ18O–NO3− and δD/δ18O–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.