Recent advances in fluorometry have led to increased use of rhodamine WT as a tracer in streams and rivers. In light of this increased use, a review of the dye's behavior in freshwater systems is presented. Studies in the groundwater literature indicate that rhodamine WT is transported nonconservatively, with sorption removing substantial amounts of tracer mass. Column studies document a two‐step breakthrough curve in which two structural isomers are chromatographically separated. Although the potential for nonconservative transport is acknowledged in the surface water literature, many studies assume that sorptive losses will not affect the characterization of physical transport processes. A literature review and modeling analysis indicates that this assumption is valid for quantification of physical properties that are based on the bulk of the tracer mass (traveltime), and invalid for the characterization of processes represented by the tracer tail (transient storage attributable to hyporheic exchange). Rhodamine WT should be considered nonconservative in the hyporheic zone due to nonconservative behavior demonstrated for similar conditions in groundwater. As such, rhodamine WT should not be used as a quantitative tracer in hyporheic zone investigations, including the study of long flow paths and the development of models describing hyporheic zone processes. Rhodamine WT may be used to qualitatively characterize storage in large systems, where there are few practical alternatives. Qualitative investigations should rely on early portions of the tracer profile, making use of the temporal resolution afforded by in situ fluorometry, while discarding later parts of the tracer profile that are adversely affected by sorption.

Researchers and practitioners alike often need to understand and characterize how water and solutes move through a stream in terms of the relative importance of in-stream and near-stream storage and transport processes. In-channel and subsurface storage processes are highly variable in space and time and difficult to measure. Storage estimates are commonly obtained using transient-storage models (TSMs) of the experimentally obtained solute-tracer test data. The TSM equations represent key transport and storage processes with a suite of numerical parameters. Parameter values are estimated via inverse modeling, in which parameter values are iteratively changed until model simulations closely match observed solute-tracer data. Several investigators have shown that TSM parameter estimates can be highly uncertain. When this is the case, parameter values cannot be used reliably to interpret stream-reach functioning. However, authors of most TSM studies do not evaluate or report parameter certainty. Here, we present a software tool linked to the One-dimensional Transport with Inflow and Storage (OTIS) model that enables researchers to conduct uncertainty analyses via Monte-Carlo parameter sampling and to visualize uncertainty and sensitivity results. We demonstrate application of our tool to 2 case studies and compare our results to output obtained from more traditional implementation of the OTIS model. We conclude by suggesting best practices for transient-storage modeling and recommend that future applications of TSMs include assessments of parameter certainty to support comparisons and more reliable interpretations of transport processes.