Tsunami-induced scour around coastal embankments and nearshore structures is a primary cause of structural instability and failure. However, the hydrodynamic mechanisms by which coastal vegetation mitigates this scour remain insufficiently understood. This study employs three-dimensional numerical simulations to investigate the influence of rigid and flexible vegetation on overflow-induced scour downstream of embankments and local scour around structures under tsunami-like inundation. The simulations were conducted using Ansys Fluent 2021R2, utilizing the Volume of Fluid (VOF) method to capture the free surface and the RNG k − ε turbulence model within the Reynolds-averaged Navier–Stokes (RANS) framework. Computational geometries were reconstructed from laboratory experiments, and the model’s reliability was validated against measured water surface profiles. The results demonstrated that vegetation significantly alters flow dynamics, velocity distributions, vortex structures, and both the magnitude and patterns of bed shear stress within scour holes. Specifically, in overflow-induced scour, vegetation suppresses scour intensity by inducing backwater effects, enhancing momentum diffusion, attenuating flow impingement on the bed, and reducing peak bed shear stress. Conversely, for local scour around structures, vegetation increases upstream water depth while intensifying downstream wake vortices, leading to scour hole elongation—particularly under dense and tall vegetation. These findings offer novel insights into the hydrodynamics of vegetation-induced scour mitigation and provide guidelines for optimizing vegetation configurations to enhance the tsunami resilience of coastal infrastructure.