We investigate the ejection of sediments from the near-bed region of a pulsating boundary layer over a flat bottom. The boundary layer flows were generated using Large Eddy Simulation (LES) while the motion of individual particles was calculated using a modified version of the Maxey and Riley equation. The suspension rate of near-bed sediment particles sharply increases during decelerating flow phase and peaks near the time of local flow reversals. This suspension pattern of sediments was closely related to the near-bed turbulent vortex structures which evolve during a wave cycle. During period of maximum flow rate, the horizontally aligned vortex cores retarded settling of sediment particles. As the flow decelerates, vertically organized vortices induce an upward flux of particles. Vertical velocity fluctuations are strongest at the time of flow reversal, leading to maximum sediment suspension at this time. These results are shown to be incompatible with simple eddy-diffusivity models for sediment transport.