The main objective of submerged breakwaters is energy dissipation of transmitted wave in leeward. In the present study, the capability of FLOW-3D and MIKE21-BW software for modeling of these structures have been investigated. In this regard, experimental results have been considered as a criterion to analyse the results of this two software. Comparison of numerical and experimental results revealed that FLOW-3D provides better results than MIKE21. Therefore, FLOW-3D has been used to investigate the effects of submerged breakwater geometry on wave transmission. In doing so, the effect of main design parameters such as shoreward slope, leeward slope, and the ratio of the width to the height of the submerged breakwaters have been studied on transmission coefficient. The results of this study show that the effect of shoreward and seaward slopes on transmission coefficient is negligible; while they considerably contribute to the wave reflection. Finally, the correlation factor has been calculated to investigate the correlation of dimensionless parameters with wave transmission coefficient. Accordingly, the most correlated parameters to wave transmission coefficient are the depth above breakwater crest to incident wave height ratio (F/H) and relative depth of breakwater (F/d), and the least correlated parameter is the breakwater slopes. The results of this study can be used in better understanding of the influential parameters in design as well as developing computation frameworks to study the submerged structures in nearshore regions.