Interactions between ecology, hydrodynamics and sediments play central roles in the evolution of coastal and freshwater ecosystems. We set out to characterise interactions of a specific hydrodynamic phenomenon – turbidity currents – with vegetation and sediment dynamics. We measured hydrodynamics and sediment deposition rates when turbidity currents flowed into plant canopies in a lock-exchange flume experiment, using simulated vegetation and three real plant species, and varying the turbidity current’s initial sediment concentration. The natural sediment used had an essentially bimodal size distribution, with coarse (6.2-104 μm) and fine (2.2-6.2 μm) fractions. In all cases, on entering the vegetation canopy, the turbidity current was initially inertially-dominated, but subsequently became drag-dominated. In the inertial regime, there was no size segregation in the deposited material. In the drag-dominated regime, the deposited material became increasingly dominated by fine sediment, at a rate dependent on the vegetation type. The transition between these two regimes occurred at a distance equivalent to 5.1 to 7.6 times the total water depth downstream of the lock gate. The size segregation of deposited sediment is posited to have consequences for substrate evolution, which in turn may affect vegetation growth. Thus, our findings point to a non-linear feedback mechanism between the spatial heterogeneity of vegetation canopies and that of the substrate they help to engineer.