Shorelines may be effectively and environmentally protected from the effects of wave action using coastal vegetation. Through numerical analysis of the Reynolds-Averaged Navier–Stokes (RANS) equations, the decrease in wave height caused by the emergence of coastal vegetation is investigated. A numerical wave tank model in three dimensions is created and simulated with REEF3D, an open-source computational fluid dynamics (CFD) program. The wave tank’s measurements are 0.70 m for length, 0.10 m for breadth, and 0.02 m for depth. Wave heights of 0.002, 0.006, and 0.007 m are simulated at a fixed wavelength of 0.1 m. The research examines a range of cylinder configurations with G/D ratios of 1, 2, and 3, where G/D stands for the gap ratio between the vegetations. These configurations include linear waves, second-order irregular waves, and fifth-order Stokes waves. Stronger wake effects and more wave attenuation are the findings of smaller G/D ratios. Lower interaction and less energy dissipation result from larger G/D ratios. The correctness and dependability of the results are validated by the analytical wave theories.