AbstractSolute transport along riparian and hyporheic flow paths is broadly expected to respond to dynamic hydrologic forcing by streams, aquifers, and hillslopes. However, direct observation of these dynamic responses is lacking, as is the relative control of geologic setting as a control on responses to dynamic hydrologic forcing. We conducted a series of four stream solute tracer injections through base flow recession in each of two watersheds with contrasting valley morphology in the H.J. Andrews Experimental Forest, monitoring tracer concentrations in the stream and in a network of shallow riparian wells in each watershed. We found hyporheic mean arrival time, temporal variance, and fraction of stream water in the bedrock‐constrained valley bottom and near large roughness elements in the wider valley bottom were not variable with discharge, suggesting minimal control by hydrologic forcing. Conversely, we observed increases in mean arrival time and temporal variance and decreasing fraction stream water with decreasing discharge near the hillslopes in the wider valley bottom. This may indicate changes in stream discharge and valley bottom hydrology control transport in less constrained locations. We detail five hydrogeomorphic responses to base flow recession to explain observed spatial and temporal patterns in the interactions between streams and their valley bottoms. Models able to account for the transition from geologically dominated processes in the near‐stream subsurface to hydrologically dominated processes near the hillslope will be required to predict solute transport and fate in valley bottoms of headwater mountain streams.