Despite regulatory measures, nitrogen contamination in groundwater remains a global environmental and health concern. Denitrifying bacteria play a crucial role, particularly in the capillary fringe, in reducing nitrogen loads through two primary pathways: heterotrophic and autolithotrophic. While the former relies on labile organic carbon as an electron donor, the latter utilizes iron sulfides that are irreversibly consumed during denitrification, making this pathway nonrenewable. In this study, we conducted high-resolution hydrogeochemical monitoring of an agricultural site for 40 months. The collected data were used to develop a solute transport model of first-order decay rates derived from continuous measurements of redox potential, allowing for partitioning denitrification processes through electron balances. We estimated a denitrification rate of 252 kg NO 3 − ha −1 a −1 and an oxidation rate of 86 kg ha −1 a −1 for iron sulfides. Moreover, we identified that the main denitrification pathway differs above and below the 200 mV isoline, with the autholitotrophic components being ≤27 and ∼60%, respectively. Overall, approximately 45% of the denitrification is autolithotrophic. Due to the limited and nonreplenishable availability of iron sulfides, this results in a downward shift of the redoxcline and ultimately to a significant loss of the denitrification potential of the soil-aquifer system.