Aquatic models used for both freshwater and marine systems frequently need to account for submerged aquatic vegetation (SAV) due to its influence on flow and water quality. Despite its importance, simplified parameterizations are generally adopted that simplify feedbacks between flow, canopy properties (e.g., considering the deflected vegetation height) and the bulk friction coefficient. This study reports the development of a fine-scale non-hydrostatic model that demonstrates the two-way effects of SAV motion interaction with the flow. An object-oriented approach is used to capture the multiphase phenomena, whereby a leaf-scale SAV model based on a discrete element method is combined with a flow-dynamics model able to resolve stresses from currents and waves. The model is verified through application to a laboratory-scale seagrass bed. A force balance analysis revealed that leaf elasticity and buoyancy are the most significant components influencing the horizontal and vertical momentum equations, respectively. The sensitivity of canopy-scale bulk friction coefficients to water depth, current speeds and vegetation density of seagrass was explored. Deeper water was also shown to lead to larger deflection of vegetation height. The model approach can contribute to improved assessment of processes influencing, water quality, sediment stabilization, carbon sequestration, and SAV restoration, thereby supporting understanding of how waterways and coasts will respond to changes brought about by development and a changing climate.