This paper shows hot to model the submerged elastic structures and adequate analysis tools for modal behavior when using finite element and boundary element method. Four different cases are reviewed depending on the location of the water and air. First case is that structures are filled with air and water is located outside. Second case is opposite to case one. These cases are solved by direct approach using collocation procedure. Third case is that water is located both sides of structures. Last case is that air is located both sides. These cases are solved by indirect approach using variational procedure. As analysis tools harmonic frequency sweep analysis and eigenvalue iteration method are selected to obtain the natural frequencies of vibrating submerged structures depending on the cases. Results are compared with closed form solutions of submerged spherical shell.