In this study, structural performance assessment of upright breakwater’s structure-foundation system using dynamic characteristics is presented. In order to achieve the objective, the following approaches are implemented. Firstly, the schematic of structural performance assessment for upright breakwater is described. The scheme consists of 1) vibration monitoring, 2) simplified analytical model, and 3) structural performance assessment. Secondly, an existing breakwater which employs caisson structure as upright part is selected as the target structural system to examine vibration-based structural performance assessment. Dynamic responses of the target structure are numerically analyzed to understand behaviors of the caisson-foundation system of the breakwater. Also, the detectability of dynamic characteristics of the system for the limited measurable condition is examined. The change of dynamic responses with respect to several parameters like wave condition, structural damage and water-level variation are analyzed. Thirdly, a vibration monitoring method is designed to measure vibration responses and modal parameters of the system which has limited sensor deployment and excitation conditions. Two output-only modal parameter extraction methods (i.e., SSI and FDD) are utilized for the extraction of modal parameters. The feasibility of the proposed vibration monitoring method is evaluated for a lab-scale test. Then, the sensitivity of the caisson-foundation system is analyzed with respect to several field parameters such as wave condition, structural damage and water-level variation. Fourthly, a simplified analytical model based on the in-situ vibration data is designed to represent the target caisson-foundation system. The caisson-foundation system is simplified into a 3-DOF model which has vertical, horizontal and rotational motions. The initial simplified model is constructed by employing the as-design information of the target breakwater. Then, the target system is identified by two-phase model update process. Fourthly, a vibration-based structural assessment method is proposed to estimate the stability and load-carrying capacity of the target caisson-foundation system. The stability is estimated from accounting the load actions of the present structural status relative to the designed structural status. Also, the load-carrying capacity is estimated by comparing strain energies and dissipated energies between the as-present status and the as-built status. Finally, the proposed structural assessment method is applied to an existing breakwater in Korea (Oryuk-do Breakwater). A part of the breakwater is selected as the target structure. In-situ vibration responses are measured and analyzed by using the vibration monitoring method. A simplified model is constructed for the target structure based on the as-design information and the in-situ measurement. The structural performance is evaluated by assessing the structural stability and the load-carrying capacity of the target structure using the vibration characteristics and the simplified model.