A numerical model of the mixing in stratified flows is developed based on the finite volume solution of the incompressible Navier-Stokes equation for a heterogeneous fluid, the continuity equation and the transport equation for solute. To incorporate the effects of small density difference on the flow field into the model with some degree of accuracy, the density variation relative to the characteristic density difference is used as one of primitive variables. The discretisation used holds the conservative property with respect to mass for the governing equations as well as the boundary conditions. The two-dimensional computation of mixing in a stratified cavity flow by a vertical circulation penetrating into the region of constant density gradient is carried out to validate the numerical model by comparing with the experiments in the previous paper. It is found that this model reproduces the deepening processes of a mixed layer in qualitative agreement with the visualization experiments in which a density interface formed by erosion of the basic density gradient suppresses the primary circulation to penetrate it. The effects of diffusivity of solute on the characteristics of the mixed layer and the stratified layer are investigated to estimate the mixing rate across the density interface.