In this study, vibration characteristics of a gravity-based caisson-foundation breakwater system are investigated for ambient and geometric parameters such as various waves, sea levels, and foundation conditions. To achieve the objective, following approaches are implemented. Firstly, operational modal analysis methods are selected to identify vibration modes from output-only dynamic responses. Secondly, a finite element model of an existing caisson-foundation breakwater system is established by using a structural analysis program, ANSYS. Thirdly, forced vibration analyses are performed on the caisson-foundation system for two types of external forces such as controlled impacts and wave-induced dynamic pressures. For the ideal impact, the wave force is converted to a triangular impulse function. For the wave flow, the wave pressure acting on the system is obtained from wave field analysis. Fourthly, vibration modes of the caisson-foundation system are identified from the forced vibration responses by combined use of the operational modal analysis methods. Finally, vibration characteristics of the caisson-foundation system are investigated under various waves, sea levels, and foundations. Relative effects of foundation conditions on vibration characteristics are distinguished from that induced by waves and sea levels.