We propose a three-dimensional non-hydrostatic shock-capturing numerical model for the simulation of wave propagation, transformation and breaking, which is based on an original integral formulation of the contravariant Navier-Stokes equations, devoid of Christoffel symbols, in general time-dependent curvilinear coordinates. A coordinate transformation maps the time-varying irregular physical domain that reproduces the complex geometries of coastal regions to a fixed uniform computational one. The advancing of the solution is performed by a second-order accurate strong stability preserving Runge-Kutta fractional-step method in which, at every stage of the method, a predictor velocity field is obtained by the shock-capturing scheme and a corrector velocity field is added to the previous one, to produce a non-hydrostatic divergence-free velocity field and update the water depth. The corrector velocity field is obtained by numerically solving a Poisson equation, expressed in integral contravariant form, by a multigrid technique which uses a four-colour Zebra Gauss-Seidel line-by-line method as smoother. Several test cases are used to verify the dispersion and shockcapturing properties of the proposed model in time-dependent curvilinear grids.