The aerodynamic properties of a canard-configuration WISES (Wing In Surface Effect Ship) flying over waves are predicted by applying the time-domain computation method based on the BEM, and the nonlinear characteristics of unsteady aerodynamic exciting forces acting on the WISES are studied through the comparison with experimental results and with linear computations reported in Part 1. Through the study it is confirmed that the presented time-domain computation considering the nonlinearity caused by the finite amplitude of waves can predict measured results more precisely compared with the linear method shown in Part 1, especially for the phase of exciting forces. The nonlinear phenomenon due to unsteady exciting forces remarkably appears in the center-of-pressure coefficient, but the amplitude of its fluctuation itself is small and not so serious for the stable flight of WISES above waves.