Very few studies have been carried out in the past in estimating bed shear stress in unsteady flows over rough channel beds. The shear velocity derived from de Saint Venant equations was compared with the steady state formulation using experimental data. The difference in shear velocities predicted by steady and unsteady formulations increases with unsteadiness of the flow. In addition, the shear velocity in accelerating flows are generally higher than that in decelerating flows and this information is very useful for sediment transport studies in unsteady flows. The error in computing shear velocity in unsteady flows using steady state formula was also quantified.