The dynamics of large-scale coherent structures (LSCS) are investigated in a rough-bed flow over the whole water column and longitudinal and transverse turbulent fluxes of momentum are compared. The relation between LSCS and fluctuations of skin friction and near-bed surface pressure is examined in order to understand the effects of LSCS on the bed. The study was carried out in an open channel with a non-moving permeable bed of screeded loose-mixed gravel (D-50 = 1.5 cm) at Reynolds numbers ranging from 3.19 x 10(4) to 1.08 x 10(5). Quasi-instantaneous full-depth three-dimensional (3D) velocity profiles with high spatial and temporal resolution measured with an acoustic Doppler velocity profiler (ADVP) are combined with the signals of a hot-film sensor mounted on the top of the gravel and a piezoresistive pressure transducer placed in the top layer of the bed particles at the centre of the channel. Vertical turbulent momentum flux is clearly dominated by ejections and sweeps over most of the water column. Near the bed, contributions of sweeps are larger than those of ejections. This is reversed at the mid-depth (z/h = 0.5). No preferential quadrant orientation is seen for the transverse momentum flux. A correlation between LSCS dynamics in the water column and data from the sensors on the bed is made evident. Sweeps correlate with positive fluctuations of bottom pressure and skin friction while ejections correlate with negative ones.