A simulation of the turbulent flow and sediment dynamics in the boundary layer originated close to the seabed by a first-order Stokes wave is performed. The flow field is obtained by the numerical integration of Navier-Stokes and continuity equations while sediment trajectories are computed via a simplified model that assumes a one-way coupling. Hence the results describe situations characterized by low concentrations and small values of the Stokes particle number. The investigation of the interaction of turbulent vortex structures with sediment shows that particles are picked up from the bed and carried into suspension when the low-speed streaks start to break up and to generate small incoherent vortices that increase mixing effects. The low-speed streaks are generated close to the seabed at the end of the accelerating phases, when the flow velocity is maximum, and breakdown during the decelerating phases of the cycle. The effects of turbulence structure and sediment characteristics on pickup and deposition rates are investigated and quantified by varying the values of the parameters which control the phenomenon.