A marine ecosystem model that incorporates nitrous oxide (N2O) production processes (i.e., ammonium oxidation during nitrification and nitrite reduction during nitrifier denitrification) and N isotopomers was developed to estimate the sea–air N2O flux and to quantify N2O production processes. This model was applied to water above the depth of 220 m at two contrasting time series sites, a subarctic station (K2) and a subtropical station (S1) in the western North Pacific. The model was validated with observed N concentration and N isotopomer data sets, and successfully simulated the higher N2O concentrations, higher δ15N values, and higher site preference values for N2O at K2 compared with S1. The annual mean N2O emissions were estimated to be 32.3 mg N m−2 year−1 at K2 and 2.7 mg N m−2 year−1 at S1. The results of case studies based on this model estimated the ratios of in situ biological N2O production to nitrate production during nitrification to be ~0.22 % at K2 and ~0.06 % at S1. It is also suggested that N2O was mainly produced via ammonium oxidation at K2, but was produced via both ammonium oxidation and nitrite reduction at S1. A large fraction (~80 %) of the ammonium oxidation at K2 was carried out by archaea in the subsurface water. Isotope tracer incubation experiments using an archaeal activity inhibitor supported this hypothesis.