Vegetation patches play an important role in controlling sediment deposition in shallow aquatic environments such as coastal saltmarshes and fluvial systems. However, predicting deposition around vegetation patches is difficult due to the complexity of patch morphology and their dynamic interaction with the flow. Here we incorporate a biomechanical model, parameterized using field data, within a 3‐D computational fluid dynamics model which allows prediction of individual shoot reconfiguration within patches due to flow forcing. The model predicts velocity attenuation and bed shear stresses within the wake of the patch which agree spatially with accretion patterns measured in the field using terrestrial lidar. The model is applied to sparse patches of Suaeda maritima, located in saltmarshes of coastal habitats, to explore the role of (I) shoot distribution, (II) patch geometry, (III) shoot flexural rigidity, and (IV) bulk flow velocity in determining the length of the predicted wake region. We demonstrate that for Suaeda maritima, with intermediate rigidity, the vertical shear layer over the vegetation controls the length of the predicted wake region. Consequently, reconfiguration due to flexural rigidity strongly impacts on wake length, confounding the relationship between patch height and wake length. A simplified model for predicting wake length based on shoot reconfiguration is applied to the simulation data and shows good agreement. The results demonstrate that the observed wake characteristics can be well explained by intraspecific variability in flexural rigidity, thus demonstrating the importance of biomechanical traits in determining flow‐vegetation‐sediment interactions.