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Spectral wave models have experienced constant development and vast improvements over the past decades. They are constantly being extended and refined in order to cover the complex wave transformation processes that take place in the coastal zone. Nevertheless, wave transmission due to overtopping has not been treated similarly yet. In this paper, a methodology to include wave generation due to overtopping in spectral wave models is presented. Incorporation of overtopping aims at better simulating the wave disturbance in the lee side of a system of offshore breakwaters and the induced hydrodynamic processes. So far, the waves generated due to wave overtopping were being neglected. The methodology consists of executing sequential simulations at small time step intervals and whenever wave overtopping occurs in a breakwater, waves are generated and transmitted in the lee side of the structure. This is achieved by modifying the boundary condition at the lee of a coastal structure to account for wave generation due to overtopping. Additionally, the transmitted spectrum source function was modified, to capture the observed transfer of energy in the higher frequencies of the spectrum due to the aforementioned overtopping process. The above methodology was implemented in the open source wave model TOMAWAC and verification with experimental measurements was carried out yielding satisfactory results. Inclusion of wave transmission due to overtopping in spectral wave models is considered to be a valuable asset, especially for the simulation of inshore hydrodynamic processes.