Temporary storage of solutes in streams is often controlled by flow-induced uptake in hyporheic zones. This phenomenon accounts for the tails that are generally observed following the passage of a solute pulse, and such exchange is particularly important for the transport of reactive substances that can be subject to various biogeochemical processes in the subsurface. Advective pumping, induced by streamflow over an irregular permeable bed, leads to a distribution of pore water flow paths in the streambed and a corresponding distribution of subsurface solute residence times. This paper describes a modeling framework that couples longitudinal solute transport in streams with solute advection along a continuous distribution of hyporheic flow paths. Moment methods are used to calculate the shape of solute breakthrough curves in the stream based on various representations of hyporheic exchange, including both advective pumping and several idealized formulations. Basic hydrodynamic principles are used to derive the distribution of solute residence times due to pumping. The model provides an accurate representation of the breakthrough curves of tritium along a 30 km reach of Säva Brook in Uppland County in Sweden. Both hydrodynamic theory for pumping exchange and pore water samples obtained from the bed during the tracer experiment suggest that the residence time for solutes in the hyporheic zone is characterized by a log normal probability density function. Closed-form solutions of the central temporal moments of solute breakthrough curves in the stream reveal a significant similarity between this new model and existing models of hyporheic exchange, including the Transient Storage Model. The new model is advantageous because its fundamentally derived exchange parameters can be expressed as functions of basic hydrodynamic quantities, which allows the model results to be generalized to conditions beyond those directly observed during tracer experiments. The utility of this approach is demonstrated by using the pumping theory to relate the spatial variation of hyporheic exchange rate along Säva Brook with the local Froude number, hydraulic conductivity and water depth.