An efficient three-dimensional non-hydrostatic model is applied to simulate free-surface waves interacting with structures. The model employs an implicit Crank-Nicholson scheme to discretize the Navier-Stokes equations under a Cartesian staggered grid framework. An integration method is introduced to account for the full effects of non-hydrostatic pressure at the free-surface layer. A domain decomposition method is proposed to effectively solve the resulting matrix system. The model is first validated by simulating three-dimensional sloshing waves in a container. The model is then applied to simulate waves propagating over two-dimensional and three-dimensional submerged structures, in which the effects of non-linearity and dispersion are important. The model results show that the model using only two vertical layers are in all favorable agreements with experimental data, demonstrating the efficiency and accuracy of the model on simulating surface waves interacting with structures. (c) 2005 Elsevier Inc. All rights reserved.