High spatial and temporal current resolution velocities were measured by use of an acoustic Doppler velocimeter (ADV) in the tidal bottom layer of North Passage Deep water Navigational Channel (DNC) of Yangtze Estuary in China. And the vertical profiles of mean velocity were measured by using a pulse-coherent acoustic Doppler profiler (PC-ADP). The measured data show the vertical profiles of mean velocity are almost logarithmic. For discussing, the turbulent kinetic energy (TKE) method based on the velocity for ADVs-based is chosen and a new logarithmic profile (LP) method ignoring the influence of complex variation of the parameter Z 0 is suggested to estimate the bed shear stresses respectively. The calculated results show that the bed shear stresses estimated by LP method are larger than the ones estimated by TKE method mostly in Yangtze estuary. At the moment of ebb peak, the maximum error can be about twice occurring and the error of ebb tide is almost greater than the one of flood tide. These phenomena are explained in this study by the deduction of formula for steady and unsteady flow. It is concluded that the vertical logarithmic profile of velocities will be influenced by unsteady flow and there is not the same bed shear stress even if there is the same logarithmic velocity profile in vertical. Generally, this has led to a necessary adjustment of the drag coefficient Cd of steady flow in flow model to avoid overestimating the bed stress for unsteady flow in estuary based on the observed data.