As the waves approach the coast, non-linearities become increasingly stronger. The interactions between the waves and loose bottoms then generate complex features within the turbulent boundary layer, which are difficult to measure and model. Experiments involving non-linear wave propagation over a mobile bed with detailed boundary layer velocity measurements and bottom elevations are presented. These data suggest a transformation in velocity time series as they are measured closer to the bed within the boundary layer with an increase in velocity skewness and a reduction in asymmetry. Additionally the vertical diffusion of momentum within the boundary layer is shown to be one order of magnitude larger than that over fixed beds. A k-omega model accounting for the measured bed level variations is used to mimic the flow in the boundary layer. In this work we present a strategy to combine bottom level variations with a k-omega model and show that it is possible to reproduce the observed experimental results. The bed vertical mobility is shown to be largely responsible for additional vertical diffusion of momentum within the boundary layer.