Wave overtopping of coastal structures has been studied using physical model experiments with rubble mound breakwaters in shallow water. The mean overtopping discharge is determined for three different foreshore slopes and various hydrodynamic conditions. The hydrodynamic results confirm that energy is transferred to low-frequency waves in very shallow water and that the short waves are in phase with the lower-frequency waves in very shallow water. As a result, the extreme waves (e.g. 2% exceedance wave height) become relatively large in very shallow water due to the energy of the low-frequency waves affecting thereby the wave overtopping. To estimate the amount of energy at the low-frequency waves, an expression is derived which reasonably accurately predicts the low-frequency wave energy (RMSE of 0.06). Considering the non-dimensional overtopping discharge, the existing formulations for the non-dimensional mean wave overtopping discharge perform poorly to reasonably in shallow water with RMSLE ranging from 1.04 to 2.92. A parameter sensitivity study shows that the short-wave steepness, relative crest height and the low-frequency wave height are the most important parameters when predicting the mean overtopping discharge in shallow water. When including the short-wave steepness and relative crest height in an empirical formulation the RMSLE for the current dataset reduces to 0.69. A further increase in accuracy is found when the low-frequency wave height and 2% exceedance wave height are included (RMSLE 0.64).