Submerged breakwaters are critical coastal defense structures. Previous studies have mainly focused on the wave dissipation performance of emerged breakwaters, while comparative research on the wave dissipation performance of submerged breakwaters in different structural forms is limited. This study investigates the hydrodynamic characteristics of three different types of submerged breakwaters: rectangular, sloping, and semicircular. Flow3D software is employed to simulate wave behavior using Reynolds-averaged Navier–Stokes (RANS) equations with a k-ε turbulence closure model. The influence of relative wave depth, wave steepness, and breakwater characteristics on hydrodynamics are analyzed. Results indicate that the transmission coefficient of the submerged breakwaters increases with relative water depth and decreases with wave steepness. The rectangular breakwater exhibits the most effective wave energy dissipation, followed by the sloping breakwater, the semicircular breakwater is least effective in wave dissipation. Meanwhile, the flow disturbance intensity around the semicircular submerged breakwater is significantly lower, approximately 75% less than the other structures. This study provides insights into the hydrodynamic behavior of different submerged breakwaters and offers a reference for the design of submerged structures.