This is a study the influence of soil carbon amendments, as part of linked laboratory experiments and field operations, for the cycling of nitrogen compounds during managed aquifer recharge (MAR). The MAR field site is in Watsonville, CA, and collects and infiltrates stormwater runoff on a working ranch. Various soil carbon amendments were applied as permeable reactive barriers (PRBs), including wood chips and almond shells, two carbon sources previously known to enhance microbially mediated denitrification. Intact soil cores were recovered from an infiltration basin and used in flow-through experiments to replicate and extend field observations to quantify substrate controls on biogeochemical processes. For laboratory experiments, PRBs included mixtures of carbon sources and native soil at specific ratios (wood chips 1:1; almond shells 1:1, 1:3, and 1:10). Almond shells mixed with soil as 50% and 25% by volume removed the most nitrate in the laboratory experiments. These two treatments also produced higher amounts of manganese and iron. Elevated levels of these trace metals are interpreted as an indication of a more reducing condition where denitrification can occur more favorably. Wood chips removed a modest amount of nitrate, but also produced nitrite, indicating incomplete denitrification. In field operations, wood chips removed more nitrate than almond shells but also produced more nitrite. Based on isotopic results, nitrite oxidation may be occurring in the wood chip treated areas. We conclude that, overall, almond shells, at a high enough amount, are a better soil amendment than wood chips for removing nitrate during infiltration for MAR.