This paper studies wave-structure interactions using an immersed boundary (IB) method in a σ coordinate non-hydrostatic wave model. In contrast to a fixed grid, the σ grid follows the movement of the free surface, which may introduce numerical errors when applying the IB method. When the grid cells located inside the structure at the previous time step move into the flow domain at the current time step, a reconstruction of velocities at the cell center is conducted to accurately estimate the fluxes at the cell faces by enforcing the no-slip boundary condition at the structure boundaries. The model is validated against experimental data in three different problems, including solitary wave interactions with rectangular obstacles, periodic wave interaction with a submerged bar and non-breaking solitary wave interactions with multiple cylinders. These test cases deal with bottom-mounted, floating as well as emergent structures with different shapes. The agreements between simulations and measurements are generally good in terms of free surface elevation, flow velocity, dynamic pressure and wave runup. It is shown that the IB method is a promising tool to simulate wave processes around structures and to predict wave/surge loads on near-coast structures.