In this paper, the fractional step approach is applied to calculation of flow in near shore area with complicated boundary shape in order to consider non-hydrostatic pressure induced by geometrical irregularities at the boundaries. At a time instant, intermediate solutions for flow velocities and free surface are obtained through the hydrostatic multi-layer calculation in the first step, and non-hydrostatic pressure field is predicted using the intermediate solutions in the second step. In the third step, final solutions are calculated considering not only hydrostatic pressure but also non-hydrostatic pressure. Present calculation algorithm with fully explicit finite difference scheme in ${sigma}$a-coordinate is successfully applied to the near shore flow calculation. Hydrostatic model is thought practically good tool enough to predict general ocean circulation problems. However, effects of non-hydrostatic pressure on flow field and free surface movements are to be emphasized, not negligible, in the vicinity of irregularities both of continental and bottom boundaries. Present method can be applied to the mesoscale free surface flows with complex bottom topography where MAC-like 3-d hydrodynamic calculations are quite ineffective and uneconomic.