In the present paper, a new calculation algorithm far solving large scale environmental or geophysical flows with free surface is proposed where the non-hydrostatic pressure component is taken into consideration. Predictor-corrector fractional step approach with explicit, forward time marching scheme in the sigma coordinate system is employed. In order to validate the present calculation algorithm and to estimate the effects of non-hydrostatic pressure on resultant flow and free surface movements, example calculations are carried out for typical steady and unsteady flow problems. Present method can be applied to the meso-scale free surface flows with complex bottom topography where MAC-like 3-d hydrodynamic calculations are quite ineffective and uneconomic.