A numerical hydrological simulation suggested that water exchange between stream channels and adjacent aquifers is enhanced by convexities and concavities in streambed topography. At St. Kevin Gulch, an effluent stream in the Rocky Mountains of Colorado, subsurface hydraulic gradients and movement of ionic tracers indicated that stream water was locally recharged into well-defined flow paths through the alluvium. Stream water-filled flow paths in the alluvium (referred to as substream flow paths) returned to the stream a short distance downstream (1 to 10 m). Recharge to the substream flow paths occurred where stream water slope increased, at the transition from pools (<1%) to steeper channel units (5–20%). Return of substream flow paths to the stream occurred where stream water slope decreased, at the transition from steeper channel units to pools. A net water flux calculation is typically used to characterize water and solute fluxes between surface and subsurface zones of catchments. Along our study reach at St. Kevin Gulch the net inflow of water from subsurface to stream (1.6 mL s⁻¹ m⁻¹) underestimated the gross inflow (2.7 mL s⁻¹ m⁻¹) by 40%. The influence of streambed topography is to enhance hydrological fluxes between stream water and subsurface zones and to prolong water-sediment contact times; these effects could have important consequences for solute transport, retention, and transformation in catchments.