The interaction of gravity waves with submerged tandem breakwater of different structural configurations is analysed in finite water depth using the Multi-Domain Boundary Element Method (MDBEM). The wave transformation characteristics, wave forces and wave energy dissipation are analysed considering the presence of impermeable type thin-walled as reef structure in front of the primary submerged breakwater. The comparative study is performed for the submerged structures of various shapes (trapezoidal, triangular, rectangular and thin-walled) and types (rubble mound, permeable, impermeable) that are designed to function together as a tandem breakwater. The effect of varying angle of incidence, relative submergence depth, and relative gap between the reef structure and primary breakwater on wave reflection and transmission are derived for the suggested tandem breakwater models. Among all the impermeable-type models, the thin-walled as reef structure designed at a distance in front of thin-walled as a primary submerged breakwater as a tandem is observed to perform efficiently in terms of energy dissipation and also offers an optimum wave transmission for both short and long wave conditions. Further, the permeable and rubble mound type trapezoidal tandem breakwater offers higher energy dissipation in comparison with all other breakwaters. In view of the design considerations and structural stability of submerged breakwaters, the addition of a reef structure acts as a defence system for the primary breakwater and also creates an energy dissipation zone that allows the shore dynamics to be preserved, making tandem models more effective in the harbour region.