Base-isolation of a primary structure generally decrease the seismic response of its own and the secondary structure. It may cause an adverse effect on the seismic response of secondary system when the system is submerged and subject to a considerable hydrodynamic effect. In flus paper, it is shown how, and how much, the base isolation of the primary structure can affect the secondary system response in extreme cases through dynamic analysis of a simplified coupled model for a submerged secondary system and a base-isolated primary structure. As an aseismatic design approach to reduce the response of the submerged system, optimization of the fluid gap, which controls the hydrodynamic mass effect, is performed. As an alternative approach in case where the control of fluid gap is unrealistic, application of base isolation to the submerged system is suggested. Effectiveness of various combinations of the primary base and secondary base isolations are compared.