Transient storage is a measure of the exchange of main channel flow with subsurface hyporheic flow and surface water dead zones. Hyporheic flow, in which river water enters the channel bed and banks to reemerge downstream, promotes biochemical processes that are important for water quality and aquatic habitat. Previous studies have quantified transient storage and hyporheic flow on small streams but were not specifically developed to identify both of these processes over long reaches of large rivers. We studied transient storage on the eighth-order upper Willamette River, which flows through high-porosity gravel deposits conducive to hyporheic flow. We used main channel dye tracer studies and solute transport modeling to estimate transient storage on nine study reaches in a 26-km-long study area. We also took dye measurements within the transient storage zone to identify transient storage flow paths. We obtained estimates of transient storage exchange coefficient, &agr;s (mean equals 1.6¿10-4 s-1), and transient storage to main channel cross-sectional area, As/A (mean equal to 0.28), that show that significant amounts of water follow flow paths with 0.2-30 hour transient storage zone residence times. Our dye measurements from the transient storage zone itself showed the occurrence of both subsurface and surface flow paths, confirming that hyporheic flow is an important component of estimated transient storage. We found that the two highest As/A estimates were for reaches that spanned the only length of active main channel in our study area that is unconstrained and where the river can rework large gravel deposits. Much of the natural channel complexity that historically promoted hyporheic flow no longer exists on the upper Willamette River. River management targeting the ecological functions provided by hyporheic flow might best focus on restoring historic hydrogeomorphic processes for creating sites conducive to hyporheic flow. ¿ 2001 American Geophysical Union