Submerged shore-parallel breakwaters for coastal defence are a good compromise between the need to mitigate the effects of waves on the coast and the ambition to ensure the preservation of the landscape and water quality. In this work we simulate, in a fully three-dimensional form, the hydrodynamic effects induced by submerged breakwaters on incident wave trains with different wave height. The proposed three-dimensional non-hydrostatic finite-volume model is based on an integral form of the Navier-Stokes equations in σ-coordinates and is able to simulate the shocks in the numerical solution related to the wave breaking. The obtained numerical results show that the hydrodynamic phenomena produced by wave-structure interaction have features of three-dimensionality (undertow), that are locally important, and emphasize the need to use a non-hydrostatic fully-three-dimensional approach.