This paper presents damage detection and estimation of stiffness parameter on a concrete scale model and a real structure of concrete pontoon using dynamic properties such as mode shapes and natural frequencies. In case of damage detection, dynamic impact test on a concrete scale model is accomplished to extract mode shapes and the practicality is verified by utilizing a damage detection technique. And the stiffness parameter of a real structure of concrete pontoon was estimated via system identification technique using the natural frequencies of the structure. The results indicate that the damaged elements of the scale model are found exactly using damage detection technique and the effective stiffness property of the real structure of concrete pontoon can be estimated by system identification technique.