In this paper, an advanced numerical model for the simulation of wave propagation and transformation in coastal areas and inside ports is presented. This model is a fully dispersive and highly nonlinear 2DH Boussinesq-type model, extended to cover real-life applications, capable of simulating the transformation of complex multi-directional irregular wave fields in coastal and harbour areas with varying bathymetries. This version of the model is coupled with wave overtopping empirical formulae as described in the EurOtop (2018) manual. The numerical model when compared with experimental data showed that a more than satisfactory agreement was achieved in most cases. A real case study, in the coastal zone of Rethymno in the Island of Crete, Greece, including the including the current port infrastructure, is also presented.