Hydrologic fluctuations and geomorphic heterogeneity are expected to produce substantial variability in solute transport within rivers. However, this variability has not been sufficiently explored due to the limited availability of solute injection data in most rivers. Here, we analyzed 81 tracer injection breakthrough curves (BTCs) along Stringer Creek, a 5.5 km2 watershed in Montana. BTC measurements were obtained for three baseflow conditions at 27 reaches along a 2600 m stream channel. BTCs in upstream reaches (first 1400 m) had receding tails with shallow slopes, indicating high solute retention. Conversely, BTCs in downstream reaches (1400 to 2600 m) had receding tails with steeper slopes, indicating low solute retention relative to upstream reaches. Difference in BTC tails along the stream channel coincided with changes in channel morphology and bedrock geology. Specifically, channel slope increases from 5–6% (upstream) to 9% (downstream), channel sinuosity decreases from a maximum of 1.32 (upstream) to 1.02 (downstream), and the underlying bedrock changes from sandstone (upstream) to granite-gneiss (downstream). Importantly, intrastream differences in BTC tails were distinctly observable only during the two lowest baseflow conditions. Spatial variability of BTC tail-slopes was most sensitive to changes in local discharge at low flow, and to changes in channel sinuosity at high flow. BTC tail-slopes varied temporally with local discharge and velocity at upstream reaches, but not at downstream reaches. These results suggest that local interactions between channel morphology and solute retention vary with hydrologic conditions, and that solute retention becomes more homogeneous at higher stream discharge.