A floating concrete pontoon is at high risk for damage and fatigue because of exposure to the marine environment loads. In this study, the dynamic properties of the structure are extracted by field test, and the stiffness of the structure is estimated through a system identification method. In addition, the stress distribution of the structure is determined by the wave loads, and the fatigue damage induced by each wave load are calculated using the estimated stiffness and DNV-code based S-N curve.