The dynamics of turbulent flows past lateral cavities is relevant for multiple environmental applications. In rivers and coastal environments, these lateral recirculating regions constitute surface storage zones, where large-scale turbulent coherent structures control the transport and fate of contaminants. Mass transport in these flows is typically represented by one-dimensional first-order equations that predict the evolution of the spatially integrated concentration between the cavity and the main channel. These models, however, cannot represent the long-term evolution of the concentration or incorporate memory effects induced by turbulence. In this investigation, we carry out large-eddy simulations (LES) of the open-channel flow with a lateral square cavity of Mignot et al. (Phys. Fluids, vol. 28, issue 4, 2016, 045104). The model is coupled with an advection–diffusion equation and a Lagrangian particle model to investigate the transport mechanisms in the cavity and across the interface. From the simulations we provide quantitative comparisons of the physical processes from both perspectives, and investigate the effects of turbulent coherent structures on residence times and trajectories from finite-time Lyapunov exponents. From the Lagrangian results, we identify general spatial distributions of time scales in the cavity associated with the dynamics of coherent structures, providing new insights into the mechanisms that drive the global transport. We also show that an upscaled model informed by LES and based on a fractional derivative captures the evolution of concentration, and the exchange between the cavity and the main channel, providing accurate predictions of mass transport and reproducing the temporal dependence observed at larger scales.