A nitrogen-based, pelagic ecosystem model has been coupled with an eddy-permitting ocean general circulation model of the Arabian Sea, and the results are compared with observations. The seasonal variability simulated by the model is in good agreement with observations: during the southwest monsoon season, phytoplankton increases in the western Arabian Sea due to upwelling along the coast; during the northeast monsoon season, phytoplankton abundance is large in the northern Arabian Sea because of the enhanced nitrate entrained by relatively deep vertical mixing. Two major differences are, however, found in the basin-wide comparison between model results and observations: an unrealistic nitrate maximum in the subsurface layer of the northern Arabian Sea and too low primary production in oligotrophic regimes. The former may be attributed to the lack of denitrification in the model. Possible causes for the latter include the present model's underestimation of fast nutrient recycling, the neglect of carbon fixation decoupled from nitrogen uptake and of nitrogen fixation, and inadequate nitrate entrainment by mixed layer deepening. The rate at which simulated nitrate increases in the northern Arabian Sea is 11–24 TgN/year, and should correspond to the denitrification rate integrated over the northern Arabian Sea assuming that the loss of nitrogen through denitrification is balanced by advective input. The model does not reproduce the observed phytoplankton bloom in the late southwest monsoon season. Possible causes are that the mixed layer may be too shallow in summer and that the horizontal transport of nitrate from the coast of Oman may be too weak. Sensitivity experiments demonstrate a strong dependence of the simulated primary productivity on the vertical mixing scheme and on the inclusion of a fast recycling loop in the ecosystem model.