In coastal areas, various types of biological and anthropic structures significantly influence the flow and related sediment dynamics. In this paper we have developed a generic flow-obstruction module, designed to represent both upward or downward, rigid or flexible structures, using a limited number of parameters. This module can be integrated to any hydrodynamic coastal model. The obstruction/flow interactions module can operate either in 3D or 2D mode. It calculates source terms used in momentum equation and in the k-e turbulent closure model (exclusive to 3D mode). Additionally, the module allows for the incorporation of multiple obstructions within a single mesh, which is invaluable when modelling realistic ecosystem dynamics. The module’s validation was carried out using flume experiments on seagrasses, as well as using numerical studies involving two anthropogenic structures: mussel long-lines and oyster tables. The coupled hydrodynamic/obstruction model yielded excellent results for 2D/3D velocity fields with minimal calibration efforts. This module offers the potential to explore the future trajectories of vulnerable coastal systems in response to global change, or to identify restoration measures in engineered coastal systems.