In this paper, a set of models responsible for hydrodynamics, sediment transport, and morphological evolution are introduced with their theoretical backgrounds, and it is explained how they are fully connected through a two‐way coupling to yield an integrated sediment transport model applicable to tsunami cases. In particular, a fully nonlinear Boussinesq model with bottom shear‐induced rotational terms is chosen for the hydrodynamic model in order to provide a better physical approximation of tsunami‐related, near‐bed hydrodynamics in the nearshore. A finite‐volume scheme, stable and suitable for phase‐resolving model runs longer than 10 simulated hours, is adopted in the numerical discretization. The accuracy and applicability of the developed model are investigated through numerical tests on various sediment problems in the shallow region. Calculated results agree well with existing experimental records. Finally, an ocean‐wide, field‐scale simulation of the 2011 Tohoku‐oki tsunami is attempted, with a focus on the localized effects of tsunami‐induced morphological changes at Crescent City Harbor and Santa Cruz Harbor (USA). Consistent with the reported observations, strong and vortical velocity fields are generated through the model and result in significant changes in morphological configurations. Depth variations and areas of scouring and deposition are compared between modelled and observed records, and the results are discussed. © 2019 John Wiley & Sons, Ltd.