We present in situ observations of near‐bed velocity profiles with high temporal and spatial resolution from a Nortek Vectrino Profiler deployed in South San Francisco Bay. Using Hilbert analysis, we ensemble‐averaged near‐bed velocity profiles by wave phase and calculated wave phase‐dependent boundary layer thickness for varying wave and current conditions. We also applied mixing length relationships to derive a boundary layer thickness‐based eddy‐viscosity and compared this estimate to one obtained from the k–ɛ turbulence model. From the eddy viscosity estimates, we find that while turbulence responds instantaneously to shear, boundary layer thickness lags by a scaling estimate based on the turbulence response timescale. This analysis provides a method for wave‐phase decomposition of field‐based velocity profile time series and shows that there is a finite‐time response between turbulence dissipation and boundary layer thickness.