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Abstract: A 3D multiple-layer σ-coordinate model has been developed to simulate surface wave interaction with various types of structures including submerged structures, immersed structures, and floating structures. This model is the extension of the earlier model [Lin P, Li CW. A σ-coordinate three-dimensional numerical model for surface wave propagation. Int J Numer Methods Fluid 2002;38(11):1045–68] that solves Navier–Stokes equations in the transformed σ-coordinate, which is especially efficient for simulation of wave propagation over varying topography. By introducing the layered σ-coordinates, the present model overcomes the difficulty encountered by the earlier model in calculating waves past a depth discontinuity, e.g., a submerged rectangular breakwater. Furthermore, with the employment of 3-layer σ-coordinate the present model is able to simulate flow interaction with an immersed body or a floating body. The new model is validated against an established Volume-Of-Fluid (VOF) model [Lin P, Liu PL-F. A numerical study of breaking waves in the surf zone. J Fluid Mech 1998;359:239–64] for the 2D solitary wave interaction with a submerged, immersed, or floating rectangular obstacle. For the solitary wave interaction with a submerged breakwater, the numerical results are also compared to the experimental data by Zhuang and Lee [A viscous rotational model for wave overtopping over marine structure. In Proc 25th Int Conf Coast Eng, ASCE, 1996. p. 2178–91] and very good agreements have been obtained for velocities in the vortex behind the structure. Finally, the present model is used to simulate 3D wave interaction with a Very Large Floating Structure (VLFS) above a submerged shoal. It is proved that the model is an accurate and efficient numerical tool to investigate different wave–structure interactions problems. [Copyright &y& Elsevier]