The paper describes the results of a two-dimensional (2-D) numerical modelling investigation of the functionality of rubble mound breakwaters with special attention focused on wave overtopping processes. The model, COBRAS-UC, is a new version of the COBRAS (Cornell Breaking Waves and Structures) based on the Volume Averaged Reynolds Average Navier–Stokes (VARANS) equations and uses a Volume of Fluid Technique (VOF) method to capture the free surface. The nature of the model equations and solving technique provides a means to simulate wave reflection, run-up, wave breaking on the slope, transmission through rubble mounds, overtopping and agitation at the protected side due to the combined effect of wave transmission and overtopping. Also, two-dimensional experimental studies are carried out to investigate the performance of the model. The computations of the free surface and pressure time series and spectra under regular and irregular waves, are compared with the experimental data reaching a very good agreement. The model is also used to reproduce instantaneous and average wave overtopping discharge. Comparisons with existing semi-empirical formulae and experimental data show a very good performance. The present model is expected to become in the near future an excellent tool for practical applications.