Acoustic Doppler velocity profiler (ADVP) measurements of instantaneous three-dimensional velocity profiles over the entire turbulent boundary layer height, δ, of rough-bed open-channel flows at moderate Reynolds numbers show the presence of large scale coherent shear stress structures (called LC3S herein) in the zones of uniformly retarded streamwise momentum. LC3S events over streamwise distances of several boundary layer thicknesses dominate the mean shear dynamics. Polymodal histograms of short streamwise velocity samples confirm the subdivision of uniform streamwise momentum into three zones also observed by Adrian et al. (J. Fluid Mech., vol. 422, 2000, p. 1). The mean streamwise dimension of the zones varies between 1δ and 2.5δ. In the intermediate region (0.2<z/δ<0.75), the contribution of conditionally sampled u'w' events to the mean vertical turbulent kinetic energy (TKE) flux as a function of threshold level H is found to be generated by LC3S events above a critical threshold level Hmax for which the ascendant net momentum flux between LC3S of ejection and sweep types is maximal. The vertical profile of Hmax is nearly constant over the intermediate region, with a value of 5 independent of the flow conditions. Very good agreement is found for all flow conditions including the free-stream shear flows studied in Adrian et al. (2000). If normalized by the squared bed friction velocity, the ascendant net momentum flux containing 90% of the mean TKE flux is equal to 20% of the shear stress due to bed friction. In the intermediate region this value is nearly constant for all flow conditions investigated herein. It can be deduced that free-surface turbulence in open-channel flows originates from processes driven by LC3S, associated with the zonal organization of streamwise momentum. The good agreement with mean quadrant distribution results in the literature implies that LC3S identified in this study are common features in the outer region of shear flows.