Measurements of transient storage in coupled surface-water and groundwater systems are widely made during base flow periods and rarely made during storm flow periods. We completed 24 sets of slug injections in three contiguous study reaches during a 1.25 year return interval storm event (discharge ranging from 21.5 to 434 L s−1) in a net gaining headwater stream within a steep, constrained valley. Repeated studies over a 9 day period characterize transient storage and channel water from prestorm conditions through storm discharge recession. Although the valley floor was always gaining from the hillslopes based on hydraulic gradients, we observed exchange of water from the stream to the valley floor throughout the study and flow conditions. Interpretations of transient storage and channel water balance are complicated by dynamic in-stream and near-stream processes. Metrics of transient storage and channel water balance were significantly different (95% confidence level) between the three study reaches and could be identified independently of stream discharge via analysis of normalized breakthrough curves. These differences suggest that the morphology of each study reach was the primary control on solute tracer transport. Unlike discharge, metrics of transient storage and channel water balance did not return to the prestorm values. We conclude that discharge alone is a poor predictor of tracer transport in stream networks during storm events. Finally, we propose a perceptual model for our study site that links hydrologic dynamics in 3-D along the hillslope-riparian-hyporheic-stream continuum, including down-valley subsurface transport.