Sand transport and morphological change occur in the wave bottom boundary layer due to sand particle interactions with an oscillatory flow and granular interactions between particles. Although these interactions depend strongly on the characteristics of the particle population, i.e. size and shape, little is known about how natural sand particles behave under oscillatory conditions and how variations in particle size influence transport behaviour. To enable this to be studied numerically, an Euler–Lagrange point-particle model is developed which can capture the individual and collective dynamics of subaqueous natural sand grains. Special treatments for particle collision, friction and hydrodynamic interactions are included to take into account the wide size and shape variations in natural sands. The model is used to simulate sand particle dynamics in two asymmetric oscillatory flow conditions corresponding to the vortex ripple experiments of Van der Werf et al. (J. Geophys. Res., vol. 112, 2007, F02012) and the sheet-flow experiments of O’Donoghue & Wright (Coast. Engng, vol. 50, 2004, pp. 117–138). A comparison of the phase resolved velocity and concentration fields shows overall excellent agreement between simulation and experiments. The particle based datasets are used to investigate the spatio-temporal dynamics of the particle-size distribution and the influence of three-dimensional vortical features on particle entrainment and suspension processes. For the first time, it is demonstrated that even for the relatively well-sorted medium-size sands considered here, the characteristics of the local grain size population exhibit significant space–time variation. Both conditions demonstrate a distinct coarse-over-fine armouring at the bed surface during low-velocity phases, which restricts the vertical mobility of finer fractions in the bed, and also results in strong pickup events involving disproportionately coarse fractions. The near-bed layer composition is seen to be very dynamic in the sheet-flow condition, while it remains coarse through most of the cycle in the vortex ripple condition. Particles in suspension spend more time sampling the upward directed parts of these flows, especially the smaller fractions, which delays particle settling and enhances the vertical size sorting of grains in suspension. For the submillimetre grain sizes considered, most particle–particle collisions occur at low impact Stokes numbers and can be expected to have low rebound velocities. The results are considered to be fundamental to the understanding of particle sorting and transport mechanisms, and can help to improve current transport modelling approaches.