A numerical model is proposed based on the time domain solution of the Boussinesq equations using the finite element method in this paper. The typical wave diffraction through a breakwater gap is simulated to validate the numerical model. Good agreements are obtained between the numerical and experimental results. Further, the effects of the wave directionality on the wave diffraction through a breakwater gap and the wave transformation on a planar bathymetry are numerically investigated. The results show that the wave directional spreading has a significant effect on the wave diffraction and refraction. However, when the directional spreading parameter s is larger than around 40, the effects of the wave directional spreading on the wave transformation can be neglected in engineering applications. A numerical model is proposed based on the time domain solution of the Boussinesq equations using the finite element method in this paper. The typical wave diffraction through a breakwater gap is simulated to validate the numerical model. Further, the effects of the wave directionality on the wave diffraction through a breakwater gap and the wave transformation on a planar bathymetry are numerically investigated. The results show that the wave directional spreading has a significant effect on the wave diffraction and refraction. However, when the directional spreading parameter s is larger than around 40, the effects of the wave directional spreading on the wave transformation can be neglected in engineering applications.