Previous studies of hyporheic zone focused largely on the net mass transfer of solutes between stream and streambed. Solute transport within the bed has attracted less attention. In this study, we combined flume experiments and numerical simulations to examine solute transport processes in a streambed with periodic bedforms. Solute originating from the stream was subjected to advective transport driven by pore water circulation due to current–bedform interactions as well as hydrodynamic dispersion in the porous bed. The experimental and numerical results showed that advection played a dominant role at the early stage of solute transport, which took place in the hyporheic zone. Downward solute transfer to the deep ambient flow zone was controlled by transverse dispersion at the later stage when the elapsed time exceeded the advective transport characteristic time tc (= L/uc with L being the bedform length and uc the characteristic pore water velocity). The advection-based pumping exchange model was found to predict reasonably well solute transfer between the overlying water and streambed at the early stage but its performance deteriorated at the later stage. With dispersion neglected, the pumping exchange model underestimated the long-term rate and total mass of solute transfer from the overlying water to the bed. Therefore both advective and dispersive transport components are essential for quantification of hyporheic exchange processes.