Turbulent oscillatory flow over sand ripples is examined using three-dimensional numerical simulations. The model solves the time-dependent Navier-Stokes equations on a curvilinear grid in a horizontally periodic domain. The flow transitions to turbulence and the presence of sand ripples increases the rate of dissipation of shoaling wave energy compared to flow over a smooth boundary. The influence of the ripple shape is shown to alter the mean flow field and affect the induced drag and dissipation rates. Shear instabilities near the boundary during phases of flow reversal resulting in vortex shedding from the ripple crest produce a continuously turbulent boundary layer, differing from results obtained in simulations over smooth boundaries.