A finite-difference scheme and a modified marker-and-cell (MAC) method are used for numerical wave tank (NWT) simulations to investigate the characteristics of nonlinear multidirectional waves. The Navier-Stokes (NS) equations are solved for two fluid layers and the boundary values updated at each time step by a finite-difference time-marching scheme in the frame of rectangular coordinate system. The fully nonlinear kinematic free-surface condition is satisfied by the density-function technique developed for two fluid layers. The directional incident waves are generated from the inflow boundary by prescribing a snakelike motion along the wavemaker direction. The outgoing waves are numerically dissipated inside an artificial damping zone located at the end of the tank. Using the NS-MAC NWT with both solid and transparent side-wall conditions, the effects of side-wall reflections are studied. Bull’s-eye waves are also numerically generated by the phase control of neighboring wavemaker segments or the reverse process of cylindrical wavemakers. The simulation results are compared with the computations by an independently developed potential-based NWT and the experiments conducted in the Offshore Technology Research Center’s 3-D wave basin.