Compared to the main channel of a stream, transient storage zones provide increased opportunity for flowing water and dissolved solutes to interact with microbial communities, both by extending residence times and by facilitating contact with biogeochemically reactive sediments. Our current understanding of transient storage has been limited by an inability to discriminate between exchange with in-channel dead zones (DZs) and with hyporheic zones (HZs). Here we present a method to distinguish stream water exchange with the DZ and HZ based on the application of a two storage zone model to conservative solute breakthrough curves (BTCs) collected from the main channel and DZs . The additional information provided by the DZ BTCs in combination with hydrometric measurements of stream velocity yields estimates of both DZ and HZ parameters. We demonstrate this approach on one 1st and one 5th order stream reach within the Ipswich River Basin, Massachusetts, USA. Our results indicate that transient storage in the 5th order reach is dominated by exchange with DZs, whereas transient storage in the 1st order reach is a combination of DZ and HZ exchange.