Hybrid dune-dike structures are innovative developments creating coastal defense systems which are more conveniently integrated with the natural environment. In this study, a numerical study was conducted to investigate the temporal evolution of wave overtopping, with the changing profile of the dune under extreme storm conditions with a constant water level, of two types of hybrid dune-dike structures in Katwijk (dike-in-dune type) and Raversijde (dune-in-front-of-dike type). XBeach 1DH was used to firstly calculate bed profiles for different time steps during a 10-h storm duration using the Surfbeat mode and then, in a second step, mean wave overtopping rates were modelled for each calculated bed profile using the Non-hydrostatic mode. According to the simulation results, most of the dune erosion occurs during the first two hours of the storm, and then continues at a slower rate as the sand deposits in front of the dune. Once the hybrid structure is eroding (so for t > 0), the significant wave height at the dike toe and the mean overtopping discharge increase in time for both Katwijk and Raversijde, although it quickly reaches a plateau for Raversijde. The first simulations with the original non-eroded profiles deviate from this trend. The reason for this deviation needs to be further investigated.