The presence of vegetation in submerged conditions and bedforms are a reality in coarse-bed streams. However, this reality has not been well investigated in the literature, despite being a major challenge for natural stream restoration. In order to control many unknown factors affecting prototype scale, this experimental study has been conducted in a laboratory flume, considering 3D bedforms. The results of this study show that 3D bedforms with submerged vegetation elements may change all estimations from 3D to 2D forms near the bed due to the change in roughness. This will change the classic determinations of resistance to flow and sediment transport via Reynolds stress and turbulent flow and may lead to more-affordable complex hydraulic process modeling.