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Simulating cross-shore sediment transport and associated sandbar migration is still a challenging task for phase-averaged coastal morphological models. Numerical studies have mostly relied on beach morphology prediction for calibration and validation, without examining in much detail the underlying hydrodynamics, sediment concentrations and transport rates. This paper reports on a new three-dimensional coastal morphodynamic model based on the hydrodynamic model of Zheng et al. (2017), combined with an advection-diffusion type suspended sediment transport model and the extended SANTOSS near-bed sediment transport formula of Van der A et al. (2013), to represent the key cross-shore transport mechanisms. The model is are calibrated based on comprehensive measurements from a large-scale laboratory experiment involving regular plunging breaking waves over an evolving sandbar, covering detailed comparisons on hydrodynamics, sediment suspension, transport rates, and bed level evolution. Separate validation using large scale wave flume experiments were also conducted to confirm the model's performance on different conditions. Good agreements are obtained between measurements and model results, which demonstrates the model's ability to reproduce cross-shore sediment transport processes under breaking waves correctly, given that the appropriate parameterizations for intra-wave processes are included. Model results also reveal the onshore near-bed transport is related to wave-induced near-bed streaming, wave skewness and asymmetry, and bed slope effects at different locations across the beach surface. Wave breaking-induced turbulence enhances the near-bed transport within the bed boundary layer which needs to be taken into account in order to achieve good model prediction skills. • A new phase-averaged morphodynamic model is developed to represent cross-shore sediment transport and beach morphology. • The model is calibrated based on comprehensive measurements to ensure good representation of all physical processes. • Model validation demonstrate the effectiveness of the model parameters for the related sediment transport processes. • Wave asymmetry and breaking turbulence to the near bed sediment onshore transport and resuspension is very important. • Detailed modelling of near bed process to include breaking turbulence to the sediment transport predictions is required. [ABSTRACT FROM AUTHOR]