The semi-empirical methods are useful tools to understand the wave overtopping phenomena, but uncertainty remains on their applicability. It’s necessary to carry out campaign surveys or laboratory tests to support them. In this paper we apply the methods proposed in the European Overtopping Manual (2007) in order to assess the flows over a vertical breakwater, marking the need to calibrate those methodologies to take into account the peculiar geometry of the structural system. This was done by introducing appropriate correction factors. The results show an improved accuracy, among numerical results and physical ones.