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In this paper a new finite-volume non-hydrostatic and shock-capturing three-dimensional model for the simulation of wave-structure interaction and hydrodynamic phenomena (wave refraction, diffraction, shoaling and breaking) is proposed. The model is basedon an integral formulation of the Navier-Stokes equations which are solved on a time dependent coordinate system: a coordinate transformation maps the varying coordinates in the physical domain to a uniform transformed space. The equationsof motionare discretized by means of a finite-volume shock-capturing numerical procedure based on high order WENO reconstructions. The solution procedure for the equationsof motionuses a third order accurate Runge-Kutta (SSPRK) fractional-step method and applies a pressure corrector formulation in order to obtain a divergence-free velocity field at each stage. The proposed model is validated against several benchmark test cases.