This paper describes the application of a three-dimensional computational fluid dynamics code to a large-scale river scheme. One of the primary aims of this paper is to provide a tool, which utilises a roughness closure derived from physical processes, requiring minimal calibration. Accordingly, a roughness closure based on the traditional drag-force approach is implemented. Unlike other implementations of this approach, the drag force is only introduced in the momentum equations and not into the turbulence closure. This ensures that the coefficients of the turbulence closure model (in this case the k−ε scheme) do not require recalibration for each application. An existing vegetated floodplain is used as a reference site and parameters characterising the dimensions of riparian vegetation and its distribution are quantified. A 100 year flood event on a considerable reach length (3500 m) of the lower River Rhine in South-West Germany is then simulated. Mean floodplain velocities are measured using dilution gauging techniques and these are compared with the computed values. Given information such as plant distribution and geometric properties of the various plant populations, the proposed tool can predict floodplain velocities, water elevation and hydrodynamic features indicative of vegetated compound channel flow.