The purpose of this work is the calibration of a numerical model for simulating the interaction of waves with a composite caisson having an internal rubble mound to dissipate incident sea wave energy. In particular, the analysis focused on the reflection coefficient and the pressure distribution at the caisson vertical walls. The numerical model is based on the Volume-Average Reynolds-Averaged Navier–Stokes (VARANS) equations. Through three closure terms (linear, nonlinear, and transition), such equations take into account some phenomena that cannot be dealt when the volume-average method is used (i.e., frictional forces, pressure force, and added mass). To reproduce properly the real phenomena, a calibration process of such terms is necessary. The reference data used in the calibration process were obtained from an experimental campaign carried out at the Hydraulics Laboratory of the University of Messina. The calibration process allowed the proper prediction of certain phenomena to be expressed as a function of different closing terms. In particular, it was estimated that the reflection coefficient and the wave loading at the frontal wall are better reproduced when all three terms are considered, while the force at the rear wall is better simulated when the effects of such terms are neglected.