In this paper a series of numerical simulations are performed to investigate the vortex shedding mechanism for a soli-tary wave propagating over a submerged breakwater by use of Reynolds averaged Navier-Stokes (RANS) model combined with a k-ε model, Flows of different Reynolds numbers up to Re=1.4×10~5 corresponding to varying incident wave heights are considered in which the characteristic fluid velocity is represented by the maximum horizontal velocity above the submerged breakwater. For the verification of the accuracy of the numerical medel, the incident waves and the veloci-ty field in the vicinity of the breakwater are compared with experimental data. The result shows that the model is capable of describing vortex shedding for a solitary wave propagating over a rectangular submerged breakwater. Key features of vortex generation, evolution and dissipation are investigated. It is found that the vortex shedding and their evolution due to separated boundary layer over the breakwater are strongly related to the Reynolds number. A considerable number of vortices and complicated vortex pattern are observed as the Reynolds number increases.