In this paper, vibration-based structural health monitoring methods that are suitable for caisson-type structures are examined by an experimental evaluation. To achieve the objective, four approaches are implemented. First, vibration-based structural health monitoring methods are selected to monitor the structural condition of caisson-type breakwaters. Second, a lab-scaled caisson structure is constructed to verify the selected monitoring methods. Third, the vibration characteristics are numerically analyzed using an FE model due to the change in the rubble mound condition. Finally, experimental vibration tests of the lab-scaled caisson structure are performed to monitor the vibration responses due to changes in rubble mound conditions and the performances of the selected methods are examined from the monitoring results.