Nitrate (NO3-) concentrations and their dual isotopic compositions (δ15N-NO3- and δ18O-NO3-) were measured to constrain N sources and their cyclic processes in summer using samples from the water column of the northern South China Sea (NSCS). Our data revealed that higher NO3- concentrations and δ15N-NO3- values were observed in the upper waters of the coastal areas near the Pearl River Estuary (PRE). The Bayesian stable isotope mixing model was used to calculated the proportion of nitrate sources, the results indicated that the nitrate in the upper waters of the coastal areas near PRE were mainly influenced by manure and sewage (63%), atmospheric deposition (19%), soil organic nitrogen (12%) and reduced N fertilizer (6%). For the upper waters of the outer areas, low NO3- concentrations and δ15N-NO3- values, but high δ18O-NO3- values, reflected that NO3- was mainly influenced by Kuroshio water intrusion (60%), atmospheric deposition (32%) and nitrogen fixation/nitrification (8%). Complex processes were found in bottom waters. Nitrification and phytoplankton assimilation may be responsible for the higher nitrate concentrations and δ15N-NO3- values. Our study, therefore, utilizes the nitrate dual isotope to help illustrate the spatial variations in nitrate sources and complex nitrogen cycles in the NSCS.