Worldwide, rubble mound breakwaters are designed and built to shelter and protect coastal areas from overtopping and flooding, especially harbours and shorelines. Rubble mound breakwaters are essential to preserve desired hydraulic conditions within the hinterland, avoiding damage to inhabited or industrial areas. This research focuses on the wave overtopping of rubble mound breakwaters as failure mechanism. To assess the wave overtopping engineers can adopt multiple methods. These methods can be ordered in increasing degree of accuracy and costs: empirical methods, neural networks, numerical models and physical laboratory experiments. The preliminary design phase is a highly iterative process. Using physical laboratory experiments within this phase is an expensive choice, therefore empirical methods are often preferred. Nevertheless, this research revealed that empirical methods, e.g. the so called EurOtop 2018, show significant shortcomings in assessing average overtopping quantities over rubble mound breakwaters, even more when the geometrical complexity of the structure increases (presence of protruding wave wall). This thesis re-calibrated the roughness coefficient proposed by the original EurOtop 2018 approach, referred to as the updated EurOtop 2018 method. Numerical models are proposed as a possible solution between empirical methods (which can be carried out quickly given their low complexity) and physical laboratory experiments (which need more time but are characterised by high accuracy). They have been increasingly used and accepted in the past decades. Following this trend, the Joint Industry Project (JIP) CoastalFOAM was launched with the objective to develop and validate a numerical model (OpenFOAM, waves2Foam, OceanWaves3D and JIP additions; referred to as CoastalFOAM) capable of accurately modelling the wave-structure interaction of rubble mound breakwaters. This research aims to calibrate and evaluate the CoastalFOAM model to assess small to large wave overtopping of rubble mound breakwaters with protruding or non-protruding wave wall, considering 500 waves. The evaluation of CoastalFOAM shows that this numerical model can be used, instead of empirical methods (e.g. updated EurOtop 2018), to assess the average overtopping discharges. CoastalFOAM showed excellent agreement with measurements for large and medium overtopping cases, while resulting less accurate for small overtopping cases. The analysis revealed, however, that the average overtopping discharge as a quantity is not capable of identifying the magnitude of large overtopping events (without modelling all 500 waves). This can be considered critical in determining whether the structure is safe enough in terms of Serviceability Limit State (SLS) or Ultimate Limit State (ULS). Consequently, this thesis proposes a new methodology to assess the maximum overtopping volume within a storm, applying the concept of wave focusing and using the NewWave theory. The input variables for the NewWave profile are extracted from the spectral properties at the toe of the breakwater. A first order wave maker is used to generate the NewWave profile, making the methodology sensitive for the degree of non-linearity of the considered wave conditions. This NewWave methodology offers improved accuracy to assess the maximum overtopping volumes when compared to the EurOtop 2018 approach. Furthermore, this research proposes to apply the inverse EurOtop 2018 technique to assess the average overtopping discharge using the NewWave maximum overtopping volume. However, the accuracy of this methodology is lower than that obtained with the updated EurOtop 2018 guidelines. This study shows that CoastalFOAM can be used, instead of the current empirical methods, to assess the average overtopping discharge within the design cycle of rubble mound breakwaters. However, according to what has emerged, CoastalFOAM shows to be less accurate in calculating small overtopping discharges as opposed to medium and large. On the other hand, when considering the maximum overtopping volume as design criterion the proposed NewWave methodology showed to be the most efficient and accurate.