A simulation of the Turkish Straits System (TSS) using a high-resolution, three-dimensional, unstructured mesh ocean circulation model with realistic atmospheric forcing for the 2008–2013 period is presented. The depth of the pycnocline between the upper and lower layers remains stationary after 6 years of integration, indicating that despite the limitations of the modelling system, the simulation maintains its realism. The solutions capture important responses to high-frequency atmospheric events such as the reversal of the upper layer flow in the Bosphorus due to southerly severe storms, i.e. blocking events, to the extent that such storms are present in the forcing dataset. The annual average circulations show two distinct patterns in the Sea of Marmara. When the wind stress maximum is localised in the central basin, the Bosphorus jet flows to the south and turns west after reaching the Bozburun Peninsula. In contrast, when the wind stress maximum increases and expands in the north–south direction, the jet deviates to the west before reaching the southern coast and forms a cyclonic gyre in the central basin. In certain years, the mean kinetic energy in the northern Sea of Marmara is found to be comparable to that of the Bosphorus inflow.