A comprehensive, continuous, point-source, dye concentration experiment was performed on the Kootenai River, Idaho, USA to describe natural river transport and mixing dynamics. Centerline fluorescent dye concentration releases formed quasi-steady state plumes. Combinations of stationary and moving observational platforms were used to describe the dye concentration plume spreading and the velocity field throughout a 550 m study reach.Observational platforms included 13 fluorescent concentration sensors, 5 acoustic Doppler profiling current meters and one acoustic Doppler velocimeter. Natural channel transverse diffusivities are calculated using concentration measurements. Observed mixing is strongly controlled and dependent on channel features. Field observations are used to initialize and validate an open source, processed-based, three-dimensional (3D) hydrodynamic model (Delft3D-FLOW). Model simulations show good agreement with the in situ measurements with velocity fields (velocity magnitude R2=0.87), water levels (R2=0.97) and concentration spread. To examine the mixing processes, prominent bathymetric features of a constriction, riffle and embayment are isolated and idealized. The numerical investigations emphasize that linear superposition of channel feature concentration spread effects does not provide accurate overall spreading estimates. Accurate concentration spreading prediction required resolving complex coupled secondary velocity fields controlled by bathymetric variability at all scales. These coherent velocity structures are responsible for the observed spatial concentration distributions, which are shown to spatially enhance and restrict lateral transport, resulting in a strongly non-linear mixing response.