A modular numerical model was developed for simulating density-stratified flow in domains with irregular bottom topography. The model was designed for examining interactions between stratified flow and topography, e.g., tidally driven flow over two-dimensional sills or internal solitary waves propagating over a shoaling bed. The model was based on the non-hydrostatic vorticity-stream function equations for a continuously stratified fluid in a rotating frame. A self-adaptive grid was adopted in the vertical coordinate, the Alternative Direction Implicit (ADI) scheme was used for the time marching equations while the Poisson equation for stream-function was solved based on the Successive Over Relaxation (SOR) iteration with the Chebyshev acceleration. The numerical techniques were described and three applications of the model were presented.