In‐stream surface storage zones (SSZs) play a significant role in the transport and fate of contaminants in rivers. Lateral recirculating areas have long residence times that favor nutrient uptake, accumulation of pollutants, and interactions with reactive sediments. In watersheds affected by acid‐mine drainage, SSZs have profound effects on biogeochemical processes, controlling the local concentration and distribution of toxic elements along the channel. Despite the importance of the turbulent flow dynamics on these processes, limited work has been carried out to analyze mass transport in natural SSZs with complex geometries. In this investigation we study a SSZ in the Lluta River, located in a high‐altitude environment in northern Chile, coupling field measurements and 3D numerical simulations to understand the transport mechanisms with the main channel. We measure the velocity field using an acoustic Doppler velocimeter (ADV) and large‐scale particle image velocimetry (LSPIV), extracting the bathymetry from digital image processing. Using this data, we perform detached‐eddy simulations (DES) to analyze the mean flow, turbulence statistics, and the dynamics of large‐scale coherent structures. From the detailed description of the turbulent flow, we study the mass exchange and the time evolution of the mean concentration in the SSZ by testing three upscaled models: A classical linear transport model, a two‐storage formulation, and a fractional transport model. The analysis integrates temporal and spatial scales to provide a new perspective on the turbulent flow in SSZs, and their effects on global mass transport in rivers.