Hyporheic exchange is an important mechanism for solute mixing between river waters and shallow groundwater in streambed sediment. The hyporheic zone also provides an important ecotone for benthic species, including macro-invertebrates, microorganisms, and parts of some fish life stages. Most hyporheic analyses are limited in scope and performed at the reach scale. This research investigates hyporheic flow induced by streambed topography at the valley-scale under different flow discharges. We use a pumping model to predict hyporheic exchange along a 35km long reach of the Deadwood River for different flow releases from Deadwood Reservoir and at different discharges from its tributaries. Hyporheic flow is primarily driven by near-bed pressure variations induced by flow and river geometry interaction in gravel bed rivers. We separate the contribution due to small-scale topography, which mainly affects dynamic head variations, and that of large-scale topography, which chiefly controls piezometric head variations. We model the former as head variations due to dune-like bedforms and the latter with the water surface elevation predicted in a 1-dimensional surface water hydraulic model. Superposition of these two energy-head components provides the boundary condition for modeling hyporheic flows, which are solved as Darcy's fluxes. In our study river, the hyporheic model shows that the mean hyporheic fluxes are mainly driven by small-scale streambed topography with limited effects of stream discharge.