In this paper, a 3D model is developed to investigate the foundation stability around breakwaters at a river mouth, where both ocean waves and river currents are considered. The present model consists of flow and seabed sub-models. In the flow sub-model, the VARANS equations is used to describe hydrodynamic process, while the dynamic u−p approximation is employed in the seabed sub-model. Based on the integrated model, both oscillatory and residual liquefaction phenomenon is investigated by adopting the poro-elastic and poro-elastoplastic seabed models, respectively. The numerical results reveal that the breakwaters at the river mouth with the river current significantly alter the hydrodynamic properties around breakwater heads. Furthermore, the dynamic soil responses and liquefaction zones predicted by the poro-elastic and poro-elastoplastic seabed models show the completely different development trend, which the latter seabed has more intense and severe reactions. The parametric study indicates that the breakwater foundation is more likely to be liquefied in a loosely deposited soil under larger waves. The river currents can exacerbate the liquefaction condition in the region near breakwater heads. In addition, the pore pressure is smaller in front of a milder slope of breakwater flank and a round breakwater head with a smooth slope.