We present results from field experiments linking hydrology, geochemistry, and microbiology during infiltration at a field site that is used for managed aquifer recharge (MAR). These experiments measured how a horizontal permeable reactive barrier (PRB) made of woodchips impacted subsurface nitrate removal and microbial ecology. Concentrations of dissolved organic carbon consistently increased in infiltrating water below the PRB, but not in un-amended native soil. The average nitrate removal rate in soils below the PRB was 1.5 g/m²/day NO₃-N, despite rapid infiltration (up to 1.9 m/d) and a short fluid residence time within the woodchips (≤6 h). In contrast, 0.09 g/m²/day NO₃-N was removed on average in native soil. Residual nitrate in infiltrating water below the PRB was enriched in δ¹⁵N and δ¹⁸O, with low and variable isotopic enrichment factors that are consistent with denitrification during rapid infiltration. Many putative denitrifying bacteria were significantly enhanced in the soil below a PRB; Methylotenera mobilis and genera Microbacterium, Polaromonas, and Novosphingobium had log₂ fold-changes of +4.9, +5.6, +7.2, and +11.8, respectively. These bacteria were present before infiltration and were not enhanced in native soil. It appears that the woodchip PRB contributed to favorable conditions in the underlying soil for enhanced nitrate removal, quantitatively shifting soil microbial ecology. These results suggest that using a horizontal PRB could improve water quality during rapid infiltration for MAR.