Vegetation meadows in coastal waters are a key constituent of a future green defense package due to the ecosystem services they provide and the potential to attenuate wave energy. To numerically describe the vegetation dynamics under wave action, this paper presents a novel application of a numerical coupling for solving fluid–elastic structure interactions (FSI) problems involving ultra-thin elements in a 3-D environment. The extended two-way coupling employed in this work combines the mesh-free Smoothed Particle Hydrodynamics (SPH) method in the DualSPHysics code to solve the fluid flow, and the Finite Element Analysis (FEA) structural solver in Project Chrono to solve the structural dynamics. To represent the vegetation, a flexible structure based on the Euler–Bernoulli beam model is used. The beam element is embedded into the SPH domain using an envelope subdomain that is discretized using dummy boundary particles. As such, this dummy envelope serves as a decoupling interface for the geometrical properties of the structure, allowing for ultra-thin structures smaller than the initial inter-particle distance (dp). The numerical approach is validated against an experimental setup including a flexible blade swaying under the action of an oscillatory flow. The results demonstrate that the numerical model is able to resolve the wave–vegetation interaction problem. Furthermore, additional insights into the blade dynamics reveal that the swaying velocity increases linearly along the length, with the upper part swaying at a speed comparable to the fluid velocity while the stem remains relatively stationary. Additionally, the findings indicate that rigid vegetation experiences higher forces per unit length, and in systems with substantial swaying motion, energy dissipation predominantly occurs around the lower base of the vegetation.