The deposition between the two adjacent submerged structures over a long time can decrease the roles of structures and also threaten the safety of the coastal communities. In this study, the reflection of the incident water waves caused by deposition among multiarrayed submerged structures are investigated by using the eigenfunction expansion method. The proper number of the steps representing a slope and the evanescent modes for calculating the reflection coefficient was suggested, and the resulting reflection coefficients were compared with the previous results. Not only the performance change due to difference styles of deposition and the amount of deposition between multi-arrayed submerged structures, but also the characteristic changes in the Bragg reflection caused by the deposition were studied. We found that the depositional topography affects the performance of multi-arrayed submerged structures. Thus, when designing multi-arrayed submerged structures, we have to consider the performance change by deposition.