Increases in reactive nitrogen from human actions have led to negative impacts on surface water (SW) and groundwater (GW) quality, and it is important to better understand denitrification processes in aquatic systems. The hyporheic zone has unique biogeochemical conditions, and is known to attenuate contaminants originating from SW and traveling through the hyporheic zone, together with necessary reactants. However, the ability of the hyporheic zone to attenuate contaminants from deeper upwelling GW plumes as they exit to SW is less understood. I used MODFLOW and SEAM3D to simulate hyporheic flow cells induced by riverbed dunes and upwelling GW together with mixing dependent denitrification of an upwelling nitrate (NO3-) plume. My basecase model scenario entailed dissolved organic carbon (DOC) and dissolved oxygen (DO) advecting from SW and DO and NO3- advecting from GW, which is typical of water in agricultural land uses. I conducted a sensitivity analysis to determine controls on mixing dependent denitrification. Mixing dependent denitrification increased with increasing hydraulic conductivity, decreasing lower bottom flux, as well as increasing DOC in SW and NO3- in GW. Non-mixing dependent denitrification also occurred when there was SW NO3-, and I found its magnitude was much greater than mixing dependent denitrification. Nevertheless, potential for hyporheic zones to attenuate upwelling NO3- plumes seems to be substantial, though highly variable depending on biogeochemical reaction rates as well as geomorphic, hydraulic and biogeochemical conditions. Stream and river restoration efforts may be able to increase both mixing and non-mixing dependent reactions by increasing hyporheic zone residence times.