The induced density-stratified fluid motion for a solitary wave past a submarine trench is investigated numerically by means of the threedimensional Navier-Stokes (N-S) solver named Truchas. The volume of fluid (VOF) method is used to trace the free surface and the transport of the lower fluid (homogeneous/dense fluid) within the trench. The numerical results were validated by comparing the computed results with laboratory experiments of Chang et al. (2011) for solitary wave induced flow motion. Then, the model is used to examine the transport processes of the various dense fluids within the trench along the vertical and horizontal directions. Particular attentions are paid to the evolution of vortex induced by solitary wave.