Soil aquifer treatment (SAT), as a gravity-based wastewater reuse process, is limited by oxygen availability to the microbial community in the soil. Using oxygen from enzymatic degradation of H2O2 to generate hyper-oxygen conditions can exceed solubility limitations associated with aeration, but little is known about the effect of hyper-oxygen conditions on the microbial community and the dominant bio-reactions. This study examined the impact of H2O2 addition on the community structure and process performance, along with SAT depth. Overall, two soil columns were incrementally fed synthetic secondary effluents to simulate infiltration through SAT. The experimental column received 14 mg/L hydrogen peroxide to double the level of natural oxygen available. The microbial kinetics of nitrifiers and heterotrophs were evaluated. We found that all of the H2O2 was degraded within the top 10 cm of the column, accompanied by a higher removal of COD (23 ± 0.25%) and ammonia (31 ± 3%) in comparison to the reference column. Higher nitrogen removal (23 ± 0.04%) was obtained for the whole process using H2O2. Analysis of nitrifiers indicated that ammonia-oxidizing bacteria were most influenced, obtaining higher concentration and abundance when exposed to H2O2. DNA sequencing analysis of samples exposed to H2O2 revealed significant community structure and diversity differences among heterotrophs. This study shows that not only aerobic, but also anoxic, microbial activity and process performance in a SAT system could be accelerated in existing infrastructure with H2O2, which could significantly decrease the associated environmental footprint.