Ocean space utilization using VLFS(Very Large Floating Structures) can provide environmental impact free space by allowing sea water flow freely through the floating structure. Use of Pontoon type VLFS for that purpose needs employment of breakwaters for reduction of wave effects. Therefore, in order to maximize advantage of environmental impact free structure, the breakwater should be the one that can allow water flow freely through it, too. In this paper hydroelastic response of a pontoon type structure is analyzed considering breakwaters which allow water flow through its opening at bottom of the breakwaters. Mode superposition technique is used for solving equation of flexible body while interactions between the pontoon and breakwaters is considered based on generalized mode concept. Bi-quadratic nine node higher-order boundary element method is adopted for more accurate numerical treatment near sharp edged body shape. Performance of various combinations of breakwaters is investigated.