The hyporheic zone is often defined as where mixing of surface water and groundwater occurs in shallow sediments beneath and adjacent to rivers. This mixing is credited with creating unique biogeochemical conditions that can attenuate contaminants from either upstream surface water or groundwater under gaining conditions. However, reactions of contaminants upwelling from groundwater may be more dependent on such mixing than contaminants from surface water. We numerically modeled mixing between hyporheic flow paths induced by riverbed dunes and flow paths of adjacent upwelling of deeper groundwater. Results show that only 12.7% or less tracer mass upwelling from deeper groundwater dispersed across into hyporheic flow paths originating in surface water. The spatial extent of a mixing-defined hyporheic zone was smaller than a hyporheic zone defined as hydrologic flow paths leaving and returning to surface water. Mixing-dependent reactions will therefore be localized within a thin mixing zone yet vary considerably with site conditions. For example, mixing in homogeneous sediments was controlled most by variation in hydraulic conductivity and upwelling flow rate which primarily affected mixing zone length. By contrast, introduction of heterogeneity increased mixing primarily by increasing mixing zone thickness, consistent with studies of flow focusing in aquifers. Finally, dispersivity is a critical parameter for which data are needed for shallow sediments. Our results help clarify hyporheic zone definitions and potential for mixing-dependent reactions. In particular, the biogeochemically reactive portion of riverbed sediments from the perspective of upwelling contaminants does not necessarily spatially coincide with more traditional hydrologic conceptions of the hyporheic zone.