Numerical simulations of turbulent oscillatory flow over a bed made of fixed, identical spherical particles have been performed. Oscillations are imposed through a shear-driven forcing by means of an harmonic velocity boundary condition on the bed. A parametric study on the effect of the particle size and Reynolds number, spanning from the laminar to the fully-turbulent regimes, has been performed. Results show that the temporal evolution of the flow over the rough bed is modified compared to the classical Stokes’ solution for smooth-wall laminar boundary layers. In the turbulent cases, the phase shift in the velocity at various distances from the bed is reduced compared to the laminar case. The phase shift reduction seems predominantly dependent on the Reynolds number rather than the bed morphology, which suggests that a unique curve may exist for large enough values of the Reynolds number. Turbulence is observed during the deceleration phases of the cycle, with the presence of a logarithmic layer in the velocity profile, and “canonical” distribution of Reynolds shear stress and turbulent kinetic energy production. During the acceleration, the logarithmic region is suppressed and the Reynolds shear stress changes sign. Nevertheless, the turbulent kinetic energy production becomes only slightly negative, because the shear is also very small during these phases. A good correlation between Reynolds and shear stresses is also evidenced from the eddy viscosity profiles, which show the presence of plateau in the outer layers approximately constant across the phases of the cycle. Turbulence in the outer layers is related to structures which develop during previous cycles and propagate from the bed to the bulk of the channel. When the flow is fully developed, anisotropy maps show similar distributions to unidirectional wall-bounded flows, while departures from canonical distributions during the transient phases are mild, because the flow responds very rapidly to the time-varying forcing.