The problem of transformation of the directional spectrum of an incident wave system over an intermediate-depth region of strongly varying 3D bottom topography is studied in the context of linear theory. The consistent coupled-mode model, developed by Athanassoulis and Belibassakis (J. Fluid Mech.389, pp. 275–301 (1999)) and extended to three dimensions by Belibassakis (Appl. Ocean Res.23(6), pp. 319–336 (2001)) is exploited for the calculation of the linear transfer function, connecting the incident wave with the wave conditions at each point in the field. This model is fully dispersive and takes into account reflection, refraction, and diffraction phenomena, without any simplification apart the standard intermediate-depth linearization. The present approach permits the calculation of spectra of all interesting wave quantities (e.g., surface elevation, velocity, pressure) at every point in the liquid domain. The application of the present model to realistic geographical areas requires a vast amount of calculations, calling for the exploitation of advanced computational technologies. In this work, a parallel implementation of the model is developed, using the message passing programming paradigm on a commodity computer cluster. In that way, a direct numerical solution is made feasible for an area of over Scripps and La Jolla submarine canyons in Southern California, where a large amount of wave measurements are available. A comparison of numerical results obtained by the present model with field measurements of free-surface frequency spectra transformation is presented, showing excellent agreement. The present approach can be extended to treat weakly nonlinear waves, and it can be further elaborated for studying wave propagation over random bottom topography.