Surface water–groundwater interaction in the hyporheic zone may enhance biogeochemical cycling in streams, and it has been hypothesized that streams exchanging more water with the hyporheic zone should have more rapid nitrate utilization. We used simultaneous conservative solute and nitrate addition tracer tests to measure transient storage (which includes hyporheic exchange and in-stream storage) and the rate of nitrate uptake along three reaches within the Red Canyon Creek watershed, Wyoming. We calibrated a one-dimensional transport model, incorporating transient storage (OTIS-P), to the conservative solute breakthrough curves and used the results to determine the degree of transient storage in each reach. The nitrate uptake length was quantified from the exponential decrease in nitrate concentration with distance during the tracer tests. Nitrate uptake along the most downstream reach of Red Canyon Creek was rapid (turnover time K−1c = 32 min), compared with nitrate uptake reported in other studies (K−1c = 12 to 551 min), but other sites within the watershed showed little nitrate retention or loss. The uptake length Sw-NO−3 for the most downstream reach was 500 m and the mass transfer coefficient Vf-NO−3 was 6·3 m min−1. Results from 15 other nitrate-addition tracer tests were used to create a regression model relating transient storage and measures of stream flow to nitrate uptake length. The model, which includes specific discharge and transient storage area, explains almost half the variability in nitrate uptake length (adjusted R2 = 0·44) and is most effective for comparing sites with very different stream characteristics. Although large differences in specific discharge and storage zone area explain inter-site differences in nitrate uptake, other unmeasured variables, such as available organic carbon and microbial community composition, are likely important for predicting differences in nitrate uptake between sites with similar specific discharge rates and storage zone areas, such as when making intra-site comparisons. Copyright © 2007 John Wiley & Sons, Ltd.