The accumulation of discharge along a stream valley is frequently assumed to be the primary control on solute transport processes. Relationships of both increasing and decreasing transient storage, and decreased gross losses of stream water have been reported with increasing discharge; however, we have yet to validate these relationships with extensive field study. We conducted transient storage and mass recovery analyses of artificial tracer studies completed for 28 contiguous 100 m reaches along a stream valley, repeated under four base-flow conditions. We calculated net and gross gains and losses, temporal moments of tracer breakthrough curves, and best fit transient storage model parameters (with uncertainty estimates) for 106 individual tracer injections. Results supported predictions that gross loss of channel water would decrease with increased discharge. However, results showed no clear relationship between discharge and transient storage, and further analysis of solute tracer methods demonstrated that the lack of this relation may be explained by uncertainty and equifinality in the transient storage model framework. Furthermore, comparison of water balance and transient storage approaches reveals complications in clear interpretation of either method due to changes in advective transport time, which sets a the temporal boundary separating transient storage and channel water balance. We have little ability to parse this limitation of solute tracer methods from the physical processes we seek to study. We suggest the combined analysis of both transient storage and channel water balance more completely characterizes transport of solutes in stream networks than can be inferred from either method alone.