Based on the numerical calculation using the eddy-resolving thermohydrodynamic model of the MHI, the fields of hydrodynamic and energy characteristics of the deep waters of the Marmara Sea averaged for the hydrological seasons of 2008 were obtained and analyzed. It is established that in winter period, at horizons from 20 to 75 m, the system consisting of mesoscale anticyclones and cyclone, as well as eddies near the northwestern and northeastern coastal regions and in the Dardanelles region, are determined by the work of the buoyancy force. In the winter-autumn period, the main contribution to the dynamic processes at the indicated depths is made by the work of the wind force. Thus, in spring and summer, the waters of the basin are involved in a mesoscale central anticyclonic vortex. In autumn, the central anticyclone, decreasing in radius, shifts to the west, and in the eastern part there is a mesoscale cyclonic vortex. In the indicated range of depths, the radii of the eddies vary from 5 to 35 km. Below 75 m the generation of dynamic structures is mainly determined by the work of the buoyancy force. In this case, the radii of the eddies vary from 7 to 16 km