U.S. Geological Survey U.S. Geological Survey Rhodamine WT dye-tracer injections in rivers of the Willamette River Basin (northwestern Oregon) yield concentration-time curves with the characteristically long times of recession suggestive of active transient storage processes. Hyporheic linkage between the surface stream and sub-surface flows is one of the possible physical mechanisms contributing to long concentration recessions. In both the Willamette and Santiam Rivers, hyporheic linkages are further suggested by detailed measurements of river discharge with an Acoustic Doppler Current Profiler, delineating zones in which water enters and leaves the surface channel. A transient storage assessment of the tracer studies has been completed using the USGS OTIS code package. In this analysis, a dimensionless parameter expresses the spatial extent of storage relative to river cross-section. In the basin-scale context of the Willamette River Basin National Water-Quality Assessment study, we conclude that the transient storage assessment is not definitive in itself, but is an additional indication of likely hyporheic linkages throughout the basin.