The hyporheic zone is the reactive interface between surface water and groundwater found beneath streams and rivers, where chemical gradients and an abundant biological presence allow beneficial attenuation of contaminants. Such attenuation often requires reactants from surface water and groundwater to mix, but few studies have explored the controls on mixing of upwelling groundwater water in the hyporheic zone and its potential to foster mixing-dependent reactions. The goals of this dissertation are therefore to evaluate the effects of (1) hydraulic controls and (2) reaction kinetic controls on hyporheic mixing and mixing-dependent reactions, and (3) use two-dimensional visualization techniques to quantify patterns of hyporheic mixing and mixing-dependent reactions. These objectives were addressed by hyporheic zone simulations using a laboratory sediment mesocosm and numerical models. In the laboratory, a hyporheic flow cell was created to observe both conservative dye mixing and abiotic mixing-dependent reaction. The numerical models MODFLOW and SEAM3D were then used to simulate the experimental data to better understand hydraulic and transport processes underlying laboratory observations and provide sensitivity analysis on hydraulic and reaction kinetic parameters. Visualization techniques showed a distinct mixing zone developing over time for both conservative and reactive conditions. Mixing zone thickness in both conditions depended on surface water head drop and the ratio of boundary inflows of surface water and groundwater (inflow ratios). The abiotic reaction caused the mixing zone to shift even under steady-state hydraulics indicating that hyporheic zone mixing-dependent reactions affect the location of mixing as chemical transformations take place. The numerical model further showed the production zone to be thicker than the mixing zone and located where reactants had already been depleted. Finally, mapping of two-dimensional microbial respiration (i.e., electron acceptor utilization) patterns in streambed sediments using dissolved oxygen and carbon dioxide planar optodes showed that coupling multiple such 2D chemical profiles can enhance understanding of microbial processes in the hyporheic zone. Temporal dynamics for these chemical species revealed development of spatial heterogeneity in microbial respiration and hence microbial activity. Our results show key hydrologic and biogeochemical controls on hyporheic mixing and mixing-dependent reactions. These reactions represent a last opportunity for attenuation of groundwater borne contaminants prior to entering surface water. / Doctor of Philosophy / The boundary between surface water and groundwater beneath streams and rivers is known to have an abundant biological presence that allows for beneficial reduction of contaminants when chemicals combine. This combination of chemicals due to mixing of the waters is an important characteristic of the boundary area (defined as the hyporheic zone). However, controls on mixing and the impact on contaminant reduction are not fully understood. Therefore, the goals of this dissertation are to evaluate (1) the effects of varying water level and flow and (2) the effects of the rates of the reaction on mixing of chemicals and chemical transformation, and (3) use two-dimensional visualization processes to quantify the reactions and mixing occurring at the boundary area of surface water and groundwater. We used both laboratory and numerical model simulations to study mixing at the boundary area. The two-dimensional visualization in both laboratory and numerical models show distinct regions where mixing occurred between the surface water and groundwater. The extent of the mixing (mixing thickness) was most dependent on the flow ratio between the upward groundwater and downward surface water. The observations were made with non-varying surface and groundwater flow rates but changes on the mixing thickness and location were seen throughout the duration of the experiments revealing that chemical reaction dynamics have an influence on the mixing process. Ultimately, these types of reactions represent a last opportunity for attenuation of groundwater borne contaminants prior to entering surface water.