In this paper we present a robust immersed boundary (IB) method for high density ratio multiphase flows that is capable of modeling complex wave-structure interaction (WSI) problems arising in marine and coastal engineering applications. The IB/WSI methodology is enabled by combining the distributed Lagrange multiplier (DLM) method of Sharma and Patankar (2005)  with a robust level set method based multiphase flow solver. The fluid solver integrates the conservative form of the variable-coefficient incompressible Navier-Stokes equations using a hybrid preconditioner and ensures consistent transport of mass and momentum at a discrete level. The consistent transport scheme preserves the numerical stability of the method in the presence of large density ratios found in problems involving air, water, and an immersed structure. The air-water interface is captured by the level set method on an Eulerian grid, whereas the free-surface piercing immersed structure is represented on a Lagrangian mesh. The Lagrangian structure is free to move on the background Cartesian grid without conforming to the grid lines. The fluid-structure interaction (FSI) coupling is mediated via Peskin's regularized delta functions in an implicit manner, which obviates the need to integrate the hydrodynamic stress tensor on the complex surface of the immersed structure. The IB/WSI numerical scheme is implemented within an adaptive mesh refinement (AMR) framework, in which the Lagrangian structure and the air-water interface are embedded on the finest mesh level to capture the thin boundary layers and the vortical structures arising from WSI. We use a well balanced gravitational force discretization that eliminates spurious velocity currents in the hydrostatic limit due to density variation in the three phases (air, water and solid). We also show that using a non-conservative and an inconsistent fluid solver can lead to catastrophic failure of the numerical scheme for large density ratio variations that are prevalent in WSI applications. An effective wave generation and absorption technique for a numerical wave tank is presented and used to simulate a benchmark case of water wave distortion due to a submerged structure. The numerical scheme is tested on several benchmark WSI problems from numerical and experimental literature in both two and three dimensions to demonstrate the applicability of the IB/WSI method to practical marine and coastal engineering problems.