Abstract: Vortex motion and sediment transport over rippled beds greatly impact coastal geomorphology, but traditional numerical models ignore important factors such as nonlinear wave-current interaction and phase-lag. The two-phase model involves complex calculations for particle collision stress, friction stress, and interphase forces, and the applications of the Lagrangian model are limited by particle size and number of particles. To minimize computational costs while ensuring accuracy, an efficient numerical model for sediment transport was developed, and the hydrodynamics and suspended sediment motion above the rippled bed under wave-current actions were explored. The efficient advection-diffusion sediment numerical model incorporated the impacts of particle inertia and wake flow around particles. The asymmetric development of boundary layer, acceleration effect, phase-lag, and mass conservation of sediment under the influence of nonlinear waves were incorporated into the bottom boundary condition for sediment. To accurately solve the flow with inverse pressure gradient above the rippled bed, the Reynolds stress was closed by the SST k-ω turbulence model. The model was verified by a series of experiments, and hydrodynamics and suspended sediment motion were studied above rippled beds under actions of current, wave, and wave-current flow. The results were as follows. (1) Compared to the wave oscillatory flow, the addition of current primarily affected the horizontal velocity above the ripple crest, while the flow below the ripple crest was still influenced by the periodic vortex structure. The positive (anticlockwise) vortex formed on the left side of the ripple moved further in the horizontal direction; the size and strength of the negative (clockwise) vortex formed on the right side of the ripple increased. The negative vortex had a longer duration and extended further on the right side, and after being thrown to the left side of the ripple, its horizontal movement distance was shorter. (2) Compared to the current flow, the presence of wave increased the turbulent viscosity, resulting in a reduction of the flow velocity gradient. The mean horizontal velocity grew slowly near the bottom and faster in the upper part. The flow velocity was distributed as two straight lines with different slopes. The intercept of the upper straight-line extension showed the apparent roughness height, which was considerably greater than the actual roughness height. (3) In wave-current flow, the distribution of concentration peaks was no longer symmetrical in the onshore and offshore phases. The third concentration peak, formed by the negative vortex carrying sediment cloud ejection during the flow reversal, was larger than the first peak formed by the positive vortex. In contrast to oscillatory flow, positive current flow altered the wave motion, promoted the development of the negative vortex, and generated net flow and net sediment transport. This study demonstrates that the presence of the wave increases the turbulent viscosity and changes the logarithmic profile of current velocity. The momentum transfer mechanism results in an apparent roughness height that is significantly greater than the actual roughness height. The presence of current mainly affects the horizontal velocity above the ripple crest and changes the wave motion. The imposed current changes the symmetry of sediment flux between onshore and offshore periods to result in net sediment transport. This efficient numerical model is suitable for the calculation of ripples under the action of waves and currents and can provide scientific guidance for the planning and construction of ports, coastal and offshore engineering projects.