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Vortex shedding for an oscillating flow over ripples is numerically investigated by solving 2-D time-dependent incompressible Navier-Stokes equations in curvilinear coordinates. The dynamics of vortex structures generated by flow separation is studied in order to understand some phenomena which take place near the bottom and in particular to get insight into the mechanism through which sediment grains are lifted up and maintained in suspension. Based on our calculated results, some important phenomena, such as vortex shedding, vortices pairing, vortices coalescence, vortex interaction with the free shear layer and so on, can be found. The behaviors of energy dissipation in the flow field and of shear stress along the ripple surface are also discussed for studying the dynamics of sediment grains in suspension and to obtain new information on the suspended load over the ripples.