The hyporheic zone is known to attenuate contaminants originating from surface water, yet the ability of the hyporheic zone to attenuate contaminants in upwelling groundwater plumes as they exit to surface water is less understood. We used MODFLOW and SEAM3D to simulate hyporheic flow cells induced by riverbed dunes and upwelling groundwater together with mixing-dependent denitrification of an upwelling nitrate (NO 2 3 ) plume. Our base case modeled labile dissolved organic carbon (DOC) and dissolved oxygen (DO) advecting from surface water, and DO and NO 2 3 advecting from groundwater, typical of certain agricultural areas. We conducted sensitivity analyses that showed mixing-dependent denitrification in the hyporheic zone increased with increasing hydraulic conductivity (K), decreasing lower boundary flux, and increasing DOC in surface water or NO 2 3 in groundwater. Surface water DOC, groundwater NO 2 3 , and K were the most sensitive parameters affecting mixing-dependent denitrification. Nonmixing-dependent denitrification also occurred when there was surface water NO 2 3 , and its magnitude was often greater than mixing-dependent denitrification. Nevertheless, mixing-dependent reactions provide functions that nonmixing-dependent reactions cannot, with potential for hyporheic zones to attenuate upwelling NO 2 3 plumes, depending on geomorphic, hydraulic, and biogeochemical conditions. Stream and river restoration efforts may be able to increase mixing-dependent reactions by promoting natural processes that promote bedform creation and augment labile carbon sources. Key Points:Mixing-dependent and nonmixingdependent denitrification in hyporheic zones is modeled Mixing-dependent denitrification is often less than nonmixingdependent Mixing-dependent denitrification increases with sediment hydraulic conductivity Correspondence to: E. T. Hester, ehester@vt.edu Citation: Hester, E. T., K. I. Young, and M. A. Widdowson (2014), Controls on mixing-dependent denitrification in hyporheic zones induced by riverbed dunes: A steady state modeling study, Water Resour. Res., 50, 9048-9066,