AbstractThe goal of this research was to compare hyporheic activity in recently restored and adjacent un‐restored reaches of the Truckee River downstream from the Reno/Sparks metropolitan area. The installation of rocky riffles and raised channel bed elevations in the restored reaches may have increased the degree of surface–subsurface interaction. A fluctuating chloride concentration signal served as the tracer, induced by the variable influx of higher salinity water several miles upstream from the study reach. The solute transport model, OTIS, was used in conjunction with the hydrodynamic model, DYNHYD5, to estimate transient storage parameters under unsteady flow conditions. The model was calibrated to chloride concentrations measured over a period of three days at six in‐stream locations representing restored and un‐restored reaches. An automated parameter estimation algorithm (SCE‐UA) was used to optimize parameters for multiple reaches simultaneously and generate a distribution of parameter estimates. Results suggest that the transient storage zone cross‐sectional area (As) is larger in the restored reaches than in the unrestored reaches, but the exchange coefficient (α) is smaller, leading to increased hyporheic residence time and hydrologic retention in the vicinity of channel reconstructions. Scenarios were used to simulate the potential effects of increased subsurface residence time on denitrification and in‐stream NO3‐N concentrations. Monte Carlo analysis was performed to assess uncertainty in the simulation results and show the potential for greater nutrient retention in the lower Truckee River as a result of channel restoration. Copyright © 2009 John Wiley & Sons, Ltd.