Abstract. We present a biogeochemical model that couples the marine nitrogen and oxygen cycles and includes euphotic, aphotic, aerobic and anaerobic processes. The model is used to investigate the mechanisms affecting nitrite and nitrogen losses in the suboxic layer of the Central Arabian Sea. In an idealized two-dimensional physical environment the model is able to reproduce the observed meridional-vertical structure of suboxic zone, secondary nitrite maximum, nitrate and oxygen. Characteristic features of vertical profiles are well represented and the modelled nitrogen transformation rates are in good agreement with observed values. The model results show that the oxygen minimum zone is not vertically homogeneous, as all suboxic processes are confined to the top 100 m of this zone. Minute differences in oxygen concentration determine the thickness of the nitrite layer. The modelled average N-loss rate in the suboxic region of the Arabian Sea is about 50 mmol N m⁻²yr⁻¹ (about 30 times smaller than most previous estimates). The system response time scale is about 50 yr, much larger than usually assumed.