Abstract The seasonal behaviour of the Black Sea–Bosphorus system is studied. The one-and-a-half-dimensional model of the Black Sea is used. It describes the level and thermohaline structure changes of the sea. A one-layer sub-model is used for the shallow Azov Sea. The Black Sea model is driven by the seasonal wind, heat flux, freshwater influx and bottom Bosphorus current. A quasi-stationary hydraulic two-layer model of the long strait with bottom and interface friction is used for Bosphorus. As opposed to most of the earlier models, it simulates exchange in terms of the level difference along the strait instead of net barotropic transport. The simulations show that the model is able to describe seasonal variations of the vertical structure of the Black Sea including cold intermediate layer (CIL) formation. A set of experiments was carried out to clarify the relative importance of seasonality of main forcing mechanisms (freshwater influx, heat budget, wind and level in the Marmara Sea) on the Black Sea vertical structure and strait exchange. The Black Sea level follows mainly in the freshwater influx with a delay of 2 months. The dependence of the volumetric flow rates in the upper and bottom layers of the strait on the level difference at the strait ends is close to linear. The simulations demonstrate sensitivity of exchange through the Bosphorus on the seasonal variations of the Marmara Sea level.