Increased nitrogen (N) from urban stormwater runoff aggravates the deterioration of aquatic ecosystems as urbanisation develops. In this study, the sources and transport of nitrate (NO3−) in urban stormwater runoff were investigated by analysing different forms of N, water isotopes (δD-H2O and δ18O-H2O), and NO3− isotopes (δ15N-NO3− and δ18O-NO3−) in urban stormwater runoff in a residential area in Hangzhou, China. The results showed that the concentrations of total N and nitrate N in road runoff were higher than those in roof runoff. Moreover, high concentrations of dissolved organic N and particulate N in road runoff led to significantly different TN concentrations in road runoff (mean: 3.76 mg/L) and roof runoff (mean: 1.23 mg/L). The high δ18O-NO3− values (mean: 60 ± 13.1‰) indicated that atmospheric deposition was the predominant NO3− source in roof runoff, as confirmed by the Bayesian isotope mixing model (SIAR model), contributing 83.6–97.8% to NO3−. The SIAR model results demonstrated that atmospheric deposition (34.2–91.9%) and chemical fertilisers (6.27–54.3%) were the main NO3− sources for the road runoff. The proportional contributions from soil and organic N were smaller than other sources in both the road runoff and roof runoff. For the initial period, the NO3− contributions from atmospheric deposition and chemical fertilisers were higher and lower, respectively, than those in the middle and late periods in road runoff during storm events 3 and 4, while an opposite trend of road runoff in storm event 7 highlighted the influence of short antecedent dry weather period. It was suggested that reducing impervious areas and more effective management of fertiliser application in urban green land areas were essential to minimize the presence of N in urban aquatic ecosystems.