The effects of waves on Surface Drag Coefficient (SDC) and surface mixing length were analyzed and discussed by carrying out three-dimensional current modeling for the Bohai Sea in the present work. A three- dimensional coupled hydrodynamical-ecological model for regional and shelf seas (COHERENS) incorporating the influences of wave-current interactions was coupled with the third-generation wave model swan taking into account time-varying currents. The effects of waves on currents were included in the SDC, surface mixing length and bottom drag coefficient. Firstly, the formulations in Donelan were incorporated into the COHERENS to account for wave-dependent SDC. In order to compare simulation results for the wave-dependent SDC, the simulation for wind-dependent SDC was also carried out. Second, Wave-Induced Surface Mixing Length (described as WISML sometimes in this paper) was incorporated into the COHERENS. Four numerical experiments were conducted to discuss the effects of two kinds of wave processes. Generally, the values of time series of current velocity and water surface elevation given by the simulation with all of the three wave processes have a good agreement with observed data. The existence of WISML changes obviously current vertical profiles and the existence of the wave dependent SDC modifies the current field of both top and bottom layers with the wind-dependent SDC.