The development of a numerical model using the fractional area/volume obstacle representation (FAVOR) method for predicting a nearshore current field bounded by complicated geometric shapes, and a three-dimensional (3D) beach evolution was described in this article. The 3D model was first tested against three cases to simulate the nearshore current fields around coastal structures, a river mouth, and a large scale cusp bathymetry. Then, the morphodynamic model tests, which are adopting the nearshore current model, were applied for the computations of beach evolution around a detached breakwater and two groins. It was confirmed that the presented model associated with the FAVOR method was useful to predict the nearshore current field in the vicinity of the complicated geometric shapes. Finally, the model was applied to a tombolo formation in a field site of Kunnui fishery port, which is located in Hokkaido, Japan.