The Baltic Sea is characterized by active water dynamics and circulation of different spatial scales, which reveal in conditions of complex bottom relief and strongly non-uniform hydrological structure. Nowadays a POM (Prinston Ocean Model) is the most popular modeling tool used as a basis for scientific and applied numerical models for the Baltic Sea. However, the disadvantages of the traditional mesoscale models are found for the thermo-hydrodynamic features, which are predicted in domains with a size less than 100 km and the grid steps less than 1 km. These features play an important role in the hydrobiological and hydrochemical processes. A proposed conservative numerical model is based on B grid finite-difference box form (Mesinger and Arakava, 1976) and constructed without traditional Bussinesque and hydrostatic assumptions. The model equations are resolved for a bottom velocity box with a real low side inclination, not with horizontal plane. It allows more realistic simulation of temporal-spatial variability for velocity and hydrological fields in the case of the complex topography and strong baroclinty. This fact is significant for the vertical velocity, which plays the important role in all processes of the water environment. This prognostic model has been applied to simulate the Baltic Sea circulation and thermohaline structures for August 2002 and to study a water circulation variability in marine area near the entrance moles of the Baltiysk-Kaliningrad ports (the Vistula Lagoon inlet), where a significant scour hole exists. Concerning the Baltic sea, an increase of level gradient and velocities component was shown in the full model version. As to area near the Vistula Lagoon outlet, the hypothesis is that strong vortex with considerable vertical currents erodes the bottom near the mole ends and makes a threat to their stability. The circulation study is necessary to analyze the ambient conditions to develop optimal measures against this destruction. the results from traditional hydrostatic model were compared with those from non-hydrostatic one in the numerical experiments with a real wind forcing (May of 2003). A model was driven by wind with direction range from south-west to west and magnitude range 4–6 m/sec within 10 hours. The horizontal grid step was 40 m. The water level difference between hydrostatic (h) and non-hydrostatic (nh) versions was found to be the largest in the area of its maximal gradients for this barotropic situation. The positive difference between nh and h versions in the rear part of the level rise shows, that the wave in the (h) case moves and decays faster. Non-hydrostatic bottom currents are larger near moles, and bottom cyclonic eddies, which may cause the erosion, are expressed better near the mole ends. Comparison with real measurements showed that water circulation pattern is formed not only by local wind but also under the influence of wind waves. Bottom eddies remain, but change their locations near the mole ends.