Several experimental studies have detected the presence of microzones in hyporheic sediments. These microzones are small scale anoxic pores, embedded within oxygen rich porous media and can act as anaerobic reaction sites producing reduction compounds such as nitrous oxide, which is a greenhouse gas. Microbes are one of the key controls on nutrient transformation in hyporheic sediment and microbial biomass growth is also capable of altering hydraulic flux in sediment, causing `bioclogging'. In this thesis, I developed one of the first computational modeling approaches that combined hydraulics and microbial kinetics to explore the presence of microzones in stream sediments. The model was used to explore stream and sediment conditions with different hydraulic flux (0.1-1.0 m/day Darcy flux), nutrient concentrations (O2=8 mg/l, Org C= 20 mg/l, NO-3= 1.5-3 mg/l NH3= 1-0.5 mg/l), and bioclogging scenarios (with and without). The model domain was constructed from a pore network model with random sized pore throat radii resulting in a heterogeneous and anisotropic flow domain that resembled a streambed, comprising of medium sand with a hydraulic conductivity of 0.8 m/day. Results indicate that microzone formation is controlled by the hydraulic flux, the nutrient concentration and bioclogging strongly inhibiting microzone formation. Bioclogging scenarios typically produced unstable microzones, which perished a few days after formation. Overall, results from the modeling show that anoxic microzones are likely to form under many hyporheic zone conditions, but their distribution and biogeochemical function will be dynamic and difficult to measure in the field. Future investigations, will need to develop field investigations capable of observing microzones to aid in further model development and validation.
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