Vertical profiles of streamwise velocity measured over bed forms are commonly used to deduce boundary shear stress for the purpose of estimating sediment transport. These profiles may be derived locally or from some sort of spatial average. Arguments for using the latter procedure are based on the assumption that spatial averaging of the momentum equation effectively removes local accelerations from the problem. Using analogies based on steady, uniform flows, it has been argued that the spatially averaged velocity profiles are approximately logarithmic and can be used to infer values of boundary shear stress. This technique of using logarithmic profiles is investigated using detailed laboratory measurements of flow structure and boundary shear stress over fixed two-dimensional bed forms. Spatial averages over the length of the bed form of mean velocity measurements at constant distances from the mean bed elevation yield vertical profiles that are highly logarithmic even though the effect of the bottom topography is observed throughout the water column. However, logarithmic fits of these averaged profiles do not yield accurate estimates of the measured total boundary shear stress. Copyright 1999 by the American Geophysical Union.