Application of transient storage models has become popular for characterizing hydrologic and biogeochemical processes in streams. The typical transient storage model represents exchange between the main channel and a single storage zone, essentially lumping together different exchange processes. Here we present a method to inform a transient storage model that accounts for two storage zones (2-SZ) to discriminate between surface transient storage (STS) exchange and exchange with hyporheic transient storage (HTS). This method requires that, in addition to tracer breakthrough curves from the main channel, cross-sectional stream velocity distributions and stream tracer concentration time series data from several main channel locations and adjacent representative STS zones be collected. We apply this method to a constant rate conservative tracer injection in a first-order stream and to an instantaneous slug conservative tracer injection in a fourth-order stream. The 2-SZ model simulations matched observed breakthrough curves of tracer concentration in the main channel and general STS behavior well. Additionally, we compared the optimized parameter sets of the 2-SZ model to one–storage zone model (1-SZ) simulations and found that the lumped storage terms of the 1-SZ model described the time scales of 2-SZ model HTS exchange and attributed the time scales of observed STS exchange to longitudinal dispersion. With additional field data collection efforts and data processing, this method can provide much more useful results than the 1-SZ approach to those interested in discriminating between surface and subsurface transient storage dynamics of streams, which is important for discerning processes important to the cycling and fate of biogeochemicals.