A numerical model is presented for simulation of hydrodynamics of a 2D vertical free surface domain consisting of an arbitrary partitioned porous and non-porous area. To this end, modified Navier–Stokes equations are considered which could be applied in surface water and in subsurface flows, simultaneously. A wide range of Reynolds number has been considered, from which non-Darcy effects have also been taken into account. A fractional step method has been used in the time discretization procedure, where the convection and diffusion terms are separated from the pressure term while solving the momentum equations. To include the variation of surface elevation in computation, the domain has been divided into two parts, namely, ‘interior subdomain’, which never gets dry during the simulation period, covered by fixed unstructured triangular grids and ‘top layer’ with only a one layer structured grid, the position of which varies with the water surface. The validation of the proposed model has been achieved by comparison of its results with both theoretical and experimental data reported in the literature.