Stream biogeochemistry is influenced by the physical and chemical processes that occur in the surrounding watershed. These processes include the mass loading of solutes from terrestrial and atmospheric sources, the physical transport of solutes within the watershed, and the transformation of solutes due to biogeochemical reactions. Research over the last two decades has identified the hyporheic zone as an important part of the stream system in which these processes occur. The hyporheic zone may be loosely defined as the porous areas of the stream bed and stream bank in which stream water mixes with shallow groundwater. Exchange of water and solutes between the stream proper and the hyporheic zone has many biogeochemical implications, due to differences in the chemical composition of surface and groundwater. For example, surface waters are typically oxidized environments with relatively high dissolved oxygen concentrations. In contrast, reducing conditions are often present in groundwater systems leading to low dissolved oxygen concentrations. Further, microbial oxidation of organic materials in groundwater leads to supersaturated concentrations of dissolved carbon dioxide relative to the atmosphere. Differences in surface and groundwater pH and temperature are also common. The hyporheic zone is therefore a mixing zone in which there are gradients in the concentrations of dissolved gasses, the concentrations of oxidized and reduced species, pH, and temperature. These gradients lead to biogeochemical reactions that ultimately affect stream water quality. Due to the complexity of these natural systems, modeling techniques are frequently employed to quantify process dynamics.