The behavior of solute transport in pool and riffle, or meandering types of streams, is greatly influenced by surface/subsurface flow and solute transport interactions. It is important to model these processes accurately in rivers and streams to improve downstream water quality. Two decades ago, Bencala and Walters (1983) [Bencala, K.E., Walters, R.A., 1983, Simulation of solute transport in a mountain pool-and-riffle stream - a transient storage model. Water Resources Research 19(3), 718-724] introduced the transient storage model to represent the movement of solute from main streams into stagnant zones and back to the main stream. This model includes the effect of both surface storage, in which water is stationary relative to the main channel and the hyporheic zone, to which water moves from the main channel, flows through and returns to the main channel. However, their simplified approach lumped the surface storage and hyporheic zones together in a single storage zone. In this study, we take a step towards a mechanistic model to explain the physics of water exchange between the surface water and the porous media by developing an improved mathematical model. For this purpose, we include the advection and dispersion processes into the transient storage zone, and we consider the hyporheic zone as a transient porous media from surface water to ground water. We use this improved model to solve a test problem in order to demonstrate its capabilities. Finally, we simulate the Uvas Creek experiment and compare our results to the observations described in Bencala and Walters (1983) [Bencala, K.E., Walters, R.A., 1983, Simulation of solute transport in a mountain pool-and-riffle stream - a transient storage model. Water Resources Research 19(3), 718-724] and to results of the existing transient storage model obtained by using OTIS. © 2006 Elsevier B.V. All rights reserved.