Traditional bed shear stress‐based models (e.g., Rouse model) derived from the classic parabolic profile of eddy viscosity in open‐channel flows fail to accurately predict suspended sediment concentration (SSC) in flows with aquatic vegetation. We developed a two‐layer, turbulence‐based model to predict SSC profiles in emergent vegetated flows. Turbulence generated from vegetation, bed, and coherent structures caused by stem‐bed‐flow interaction are considered into the near‐bed turbulent kinetic energy (TKE) to calculate the effective bed shear velocity, ubeff*. The model, validated by experimental data, further showed that the thickness height of the near‐bed layer (effective bottom boundary layer), Hb, varies with flow velocity and canopy density. Two additional models are provided to estimate Hb and ubeff*. The model is expected to provide critical information to future studies on sediment transport, landscape evolution, and water quality management in vegetated streams, wetlands, and estuaries.