The transport of sediment in regions with vegetation plays an important role in aquatic ecosystems and landform evolution in river deltas. In this study, flow parameters and suspended sediment concentration (SSC) within an emergent canopy with real plant morphology (Typha latifolia) were measured in a laboratory channel. T. latifolia is a common marsh species with multiple thin leaves emerging from a tight bundle (culm) at the bed. The observed equilibrium SSC profile differed significantly from a Rouse profile, the classic model for SSC over bare beds. The vertical distribution of SSC was nearly uniform in the culm region of the canopy, and decreased with height in the upper canopy region of distributed leaves. The profile of SSC reflected the vertically nonuniform turbulent diffusion, which arose from the plant morphology. A diffusivity model based on cylinder arrays was first validated with tracer data and then adapted to the T. latifolia morphology, providing a way to model turbulent diffusivity in marsh systems. The diffusivity model was successfully used within a random displacement model to predict the spatial evolution and equilibrium SSC profile within the T. latifolia canopy. Key Points Profiles of suspended sediment concentration (SSC) were measured in a model canopy of Typha latifolia The vertical turbulent diffusivity depends on plant‐generated turbulence and morphology A model to predict vertical diffusivity was developed, validated, and used to simulate the SSC with a random displacement model