Wind-induced waves can lead to the partial or complete wash-over of beaches, causing erosion that impacts both the landscape and tourist infrastructure. In some regions of the world, e.g., Croatia, this process, which usually occurs during a harsh winter, has a major impact on the environment and the economy, and preventing or reducing this process is highly desirable. One of the simplest methods to reduce or prevent beach erosion is the use of innovative underwater structures designed to decrease wave energy by reducing wave height. In this study, submerged breakwaters are numerically investigated using various topologies, positions, and angles relative to the free surface. Not only is the optimal topology determined, but the most efficient arrangement of multiple breakwaters is also determined. The advantage of newly developed submerged breakwaters over traditional ones (rock-fixed piers) is that they do not require complex construction, massive foundations, or high investment costs. Instead, they comprise simple floating bodies connected to the seabed by mooring lines. This design makes them not only cheap, adaptable, and easy to install but also environmentally friendly, as they have little impact on the seabed and the environment. To evaluate wave damping effectiveness, the incompressible computational fluid dynamics (ICFD) method is used, which enables the use of a turbulence model and the possibility of accurate wave modelling.