Numerical models with hydrostatic pressure have been widely utilized in studying flows in rivers, estuaries and coastal areas. The hydrostatic assumption is valid for the large-scale surface flows where the vertical acceleration can be ignored, but for some particular cases the hydrodynamic pressure is important. In this paper, a vertical 2D mathematical model with non-hydrostatic pressure was implemented in the σ coordinate. A fractional step method was used to enable the pressure to be decomposed into hydrostatic and hydrodynamic components and the predictor-corrector approach was applied to integration in time domain. Finally, several computational cases were studied to validate the importance of contributions of the hydrodynamic pressure. Numerical models with hydrostatic pressure have been widely utilized in studying flows in rivers, estuaries and coastal areas. The hydrostatic assumption is valid for the large-scale surface flows where the vertical acceleration can be ignored, but for some particular cases the hydrodynamic pressure is important In this paper, a vertical 2D mathematical model with non-hydrostatic pressure was implemented in the σ coordinate. A fractional step method was used to enable the pressure to be decomposed into hydrostatic and hydrodynamic components and the predictor-corrector approach was applied to integration in time domain. Finally, several computational cases were studied to validate the importance of contributions of the hydrodynamic pressure.