AbstractBecause of the influence of various storage zones, solute transport in a stream channel cannot be interpreted by advection and dispersion processes alone. Thus, in recent decades, various models that incorporate storage‐zone effects have been proposed to characterize anomalous storage mechanisms. The validity of these models has been predominantly demonstrated using tracer breakthrough curves measured in surface flow. However, the storage effect is usually less influential on the breakthrough curve behavior than in‐stream flow dynamics. Thus, for model validation, the tracer behavior within the storage zone should be investigated separately. The present study aims to quantify the time‐dependent storage effect, herein termed the net retention time distribution (NRTD), from tracer measurements in the flow zone using a deconvolution technique with manipulation in the Fourier domain. The results demonstrated that the deconvolved NRTDs successfully represented the temporal behavior of the tracer in the storage zones without significant distortion in the primary information of the observed breakthrough curves. Using estimates of NRTD, we evaluated the simulations of the transient storage model, and found that the storage effects were underestimated as much as an average 18.5% in this study. The deconvolved NRTDs were also utilized to predict the biodegradation losses of organic chemicals flowing along a stream at confidence intervals.