Large-scale flow structures (LSFS) in the streamwise direction are important features of gravel-bed river flows, because they may contribute to sediment transport and gas exchange. In the present study, these structures are detected using Huang's empirical mode decomposition and reconstructed with phase-averaging techniques based on a Hilbert transform of the velocity signal. The analysis is based on the fluctuating component of 15 quasi-instantaneous velocity profiles measured with a three-dimensional (3D) acoustic Doppler velocity profiler (ADVP) in an armoured gravel-bed river with a low relative submergence of 2.9 (ratio between flow depth and bed grain diameter). LSFS were identified in most of the measured profiles and consistently showed similar features. We were able to characterize the geometry of these large-scale coherent structures: the front has a vertical linear shift in the time domain and a vertical profile corresponding to a first quarter moon with the apex situated at z/h ≈ 0.4. In the vertical, the front scales with flow depth h, and in the streamwise direction, LSFS scale with three to seven times the mean flow depth. On the bed, the effect of LSFS is a periodic non-linear variation of the friction velocity on average between 0.90 and 1.10 times the mean value. A model for the friction velocity cycle resulting from LSFS oscillation is presented. Copyright © 2014 John Wiley & Sons, Ltd.