Historical oceanographic data from the period 1964-1997 from two deep subbasins (the Gotland Deep and the Landsort Deep) in the Baltic Sea have been analyzed, by using a budget method on stagnant periods, with respect to vertical diffusion and vertical energy flux density in the deep water. It was found that the rate of deepwater mixing varied with the seasons, with higher rates in fall and winter compared to spring and summer. Further, according to the analyzed data, the downward flux density of energy available for vertical diffusion decreased with increasing depth in the Gotland Deep. In the Landsort Deep, however, the flux density increased somewhat, probably because of topographic concentration of the energy, before decreasing toward the bottom. Moreover, the vertical energy flux densities were compared with the expected flux density from the local wind. It is proposed that in the Gotland Deep, which is outside the coastal boundary layer, the observed deepwater mixing is dominated by the energy input from the wind via inertial currents and internal waves. In the Landsort Deep, however, which is within the coastal boundary layer, the expected flux density of energy from the local wind cannot explain the observed rate of work against the buoyancy forces. It is proposed that the active coastal boundary layer plays a central role in the transfer of energy to mixing processes in the deep water.