Shear velocity u() is an important parameter in geophysical flows, in particular with respect to sediment transport dynamics. In this study, we investigate the feasibility of applying five standard methods [the logarithmic mean velocity profile, the Reynolds stress profile, the turbulent kinetic energy (TKE) profile, the wall similarity and spectral methods] that were initially developed to estimate shear velocity in smooth bed flow to turbulent flow over a loose bed of coarse gravel (D-50=15cm) under sub-threshold conditions. The analysis is based on quasi-instantaneous three-dimensional (3D) full depth velocity profiles with high spatial and temporal resolution that were measured with an Acoustic Doppler Velocity Profiler (ADVP) in an open channel. The results of the analysis confirm the importance of detailed velocity profile measurements for the determination of shear velocity in rough-bed flows. Results from all methods fall into a range of +/- 20% variability and no systematic trend between methods was observed. Local and temporal variation in the loose bed roughness may contribute to the variability of the logarithmic profile method results. Estimates obtained from the TKE and Reynolds stress methods reasonably agree. Most results from the wall similarity method are within 10% of those obtained by the TKE and Reynolds stress methods. The spectral method was difficult to use since the spectral energy of the vertical velocity component strongly increased with distance from the bed in the inner layer. This made the choice of the reference level problematic. Mean shear stress for all experiments follows a quadratic relationship with the mean velocity in the flow. The wall similarity method appears to be a promising tool for estimating shear velocity under rough-bed flow conditions and in field studies where other methods may be difficult to apply. This method allows for the determination of u() from a single point measurement at one level in the intermediate range (036). Copyright (c) 2013 John Wiley & Sons, Ltd.