Reliable estimation of wave run-up is required for the effective and efficient design of coastal structures when flooding or wave overtopping volumes are an important consideration in the design process. In this study, a unified formula for the wave run-up on bermed structures has been developed using collected and existing data. As data on berm breakwaters was highly limited, physical model tests were conducted and the run-up was measured. Conventional governing parameters and influencing factors were then used to predict the dimensionless run-up level with 2% exceedance probability. The developed formula includes the effect of water depth which is required in understanding the influence of sea level rise and consequent changes of wave height to water depth ratio on the future hydraulic performance of the structures. The accuracy measures such as RMSE and Bias indicated that the developed formula is more accurate than the existing formulas. Additionally, the new formula was validated using field measurements and its superiority was observed when compared to the existing prediction formulas. Finally, the new design formula incorporating the partial safety factor was introduced as a design tool for engineers.