Reconstructing past changes in the oceanic nitrate inventory with sedimentary N records in the South China Sea (SCS), which is the terminal of North Pacific Intermediate Water (NPIW), has regional and global implications. However, water-column nitrate cycling that affects N isotope preservation remains poorly understood in the SCS. We present a new dataset of nitrate isotopes (δ¹⁵N_NO3 and δ¹⁸O_NO3) to elucidate nitrate dynamics in the SCS and the adjoining western North Pacific Ocean (wNPO). Greater increases in δ¹⁸O_NO3 than in δ¹⁵N_NO3 are observed in the SCS euphotic zone, suggesting a combined effect of partial nitrate assimilation and nitrification. In the subsurface and thermocline waters of both regions, upward disproportional decreases in δ¹⁵N_NO3 and δ¹⁸O_NO3 accompanied by elevated nitrate anomalies (N*) indicate an accumulation of external N. Such changes are less significant in the SCS due to higher nitrate concentrations therein, although external N influxes are comparable in both regions. High δ¹⁵N_NO3 and δ¹⁸O_NO3 values in the wNPO intermediate water result from the lateral transport of NPIW with isotopically more enriched nitrate from the remote denitrification zones followed by mixing with overlying water containing isotopically depleted nitrate. As NPIW flows into the SCS, its isotopically enriched signal is further diluted by strong vertical mixing with overlying and underlying waters in the interior. Compared to its source water from the wNPO, the SCS deep water has consistent nitrate isotopic compositions but significantly lower N*, indicating increased benthic denitrification at the wNPO margins with an estimated rate of 0.26–0.41 mmol N m^–2 day^–1.