The goal of this research was to compare estimated volumes and rates of hyporheic exchange 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 may increase the degree of surface-subsurface interaction which could lead to greater denitrification in anoxic subsurface zones. Due to the size of the Truckee River (annual average flow of 800 cfs), the volume of solute or dye needed to perform a typical tracer injection test would be formidable. Instead, a fluctuating chloride concentration serves as the tracer, induced by the variable influx of treated effluent from the Truckee Meadows Water Reclamation Facility (TMWRF), located 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 data sets simultaneously and generate a distribution of parameter estimates. Results suggest that the transient storage zone (A _s) is larger in the restored reaches than in the unrestored reaches, but the exchange rate (α) is smaller, leading to increased hyporheic residence times in the vicinity of channel reconstructions. Scenarios were used to simulate the 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.