Stream hydraulics control flux into and out of slow-moving water transient storage (WTS) zones and, thus, hydrologic retention in stream channels. In-stream nutrient uptake is thought to depend on hydrologic retention, so stream hydraulics could influence the extent to which in-stream nutrient biogeochemistry affects nutrient export downstream. Our goals were to: 1) characterize WTS with an emphasis on water residence time and 2) evaluate its influence on nutrient uptake. We analyzed data from 2 y of monthly solute-tracer injections with accompanying nutrient-uptake estimates in 2 hydrogeomorphically different streams. We fit the conservative tracer breakthrough curves to 2 hydrodynamic models: the one-dimensional transport with inflow and storage (OTIS) and the stochastic mobile–immobile model (SMIM), which allows for a wide distribution of water residence times. The 2 streams differed hydraulically, especially in water residence-time distributions in WTS zones. SMIM parameters depended less on discharge than did OTIS parameters, indicating that SMIM may be influenced more by local features of channel morphology than by hydrologic conditions. NH4+ uptake differed between streams, was correlated with all SMIM hydraulic parameters, and was weakly correlated with only 1 OTIS parameter. Based on SMIM correlations, the parameters related to the exchange of free-flowing water with water storage zones and the in-stream retention times explained 43 and 41%, respectively, of the variation in NH4+ uptake in the streams. Soluble reactive P (SRP) uptake was similar between streams and was not correlated with hydraulic parameters. These results indicate that hydraulics and residence time of water can be important regulators of WTS zones and nutrient uptake in headwater streams, but other environmental factors must be considered for complete understanding of in-stream nutrient processing capacity.