In this study, the wave profiles and kinematics of highly nonlinear waves at various water depths were calculated using a 2D fully nonlinear Numerical Wave Tank (NWT). The NWT was developed based on the Boundary Element Method (BEM) with the potential theory and the mixed Eulerian-Lagrangian (MEL) time marching scheme by 4th-order Runge-Kutta time integration. The spatial variation of intermediate-depth waves along the direction of wave propagation was caused by the unintended generation of 2nd-order free waves, which were originally investigated both theoretically and experimentally by Goda (1998). These free waves were induced by the mismatch between the linear motion of wave maker and nonlinear displacement of water particles adjacent to the maker. When the 2nd-order wave maker motion was applied, the spatial modulation of the waves caused by the free waves was not observed. The respective magnitudes of the nonlinear wave components for various water depths were compared. It was found that the high-order wave components greatly increase as the water depth decreases. The wave kinematics at various locations were calculated and compared with the linear and the Stokes 2nd-order theories.