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Abstract Turbulence‐resolving simulations elucidate key elements of fluid dynamics and sediment transport in fluvial environments. This research presents a feasible strategy for applying state‐of‐the‐art computational fluid mechanics to the study of sediment transport and morphodynamic processes in lateral separation zones, which are common features in canyon rivers where massive lateral flow separation causes large‐scale turbulence that controls sediment erosion and deposition. An eddy‐resolving model was developed and tested at the field‐scale, coupling a viscous flow and sediment transport solver using Detached Eddy Simulation techniques. A morphodynamic model was applied to the viscous flow/sediment solver to calculate erosion and deposition. A simulation of turbulence was performed at the grid resolution for a straight channel to determine the relative contributions of modeled and resolved diffusivity. The time‐dependent, energetically important, correlative, non‐stationary signals of the simulated quantities were captured at the lateral separation zone. Strong periodic signals featured by high amplitude were found at the separation zone, while low frequency pulsations were observed at the reattachment zone of the lateral separation zone. Interactions between the eddies and the loose bed boundaries resulted in erosion of sediment at the main channel followed by deposition at the primary eddy and eddy bars.