© 2014 Elsevier Ltd. Numerical simulations are performed to investigate the flow evolution of a depression ISW generated by gravity collapse in a fluid system with a density pycnocline. A finite volume based Cartesian grid method is adopted to directly resolve the Navier-Stokes equations and the general mass continuity equation. Results of the numerical computation are validated by comparing with that of laboratory experiment. Numerical results reveal the initial vortex remains identical for the same step depth but the decrease in its strength is significant as the depth of upper layer increases. However, step depth influences the vertical structure of the initial vortex more than the upper/lower layer depth ratio does on wave generation.