A three-dimensional model that couples Reynolds–averaged Navier–Stokes equations with an advection–diffusion solver for flow and concentration fields over a fixed, non-permeable boundary is presented. The model simulates oscillatory flow over a wavy wall with a constant scalar source to assess the effects of a boundary-induced pressure gradient on passive scalar mixing. Results were compared to experimental data collected in an oscillating tray facility. Hydrodynamic quantities are in favourable agreement with observations. The model captured vortex dynamics correctly, and turbulence statistics were modelled reasonably well. Comparisons of time-resolved and bulk scalar quantities for crest and trough sources were in favourable agreement with observations. Results indicate that the model can be utilized to study processes with highly intermittent phenomena, such as the transport of wastes and dissolved nutrients in the coastal bottom.