© Copyright © 2019 Bouskill, Conrad, Bill, Brodie, Cheng, Hobson, Forbes, Casciotti and Williams. The capillary fringe is a subsurface terrestrial-aquatic interface that can be a significant hotspot for biogeochemical cycling of terrestrially derived organic matter and nutrients. However, pathways of nitrogen (N) cycling within this environment are poorly understood, and observations of temporal fluctuations in nitrate (NO3−) concentrations lack the necessary resolution to partition between biotic or abiotic mechanisms. At discrete sampling points we measured NO3−, nitrite (NO2−), ammonium (NH4+), gaseous nitrous oxide (N2O), and nitrogen (N2), and the corresponding isotopic composition of NO3− within floodplain sediments at Rifle, Colorado. Coincident with an annually reoccurring spring/summer excursion in groundwater elevation driven by snowmelt, we observed a rapid decline in NO3− followed by transient peaks in NO2−, at three depths (2, 2.5, and 3 m) below the ground surface. Isotopic measurements (δ15N and δ18O of NO3−) suggest an immediate onset of biological N loss at 2 m. At 2.5 and 3 m, NO3− concentrations declined initially with no observable isotopic response, indicating dilution of NO3− as the NO3−-deficient groundwater rose, followed by denitrification after prolonged saturation. A simple Rayleigh model further supports this depth-dependent variability in the significance of actively fractionating mechanisms (i.e., NO3− reduction) relative to non-fractionating mechanisms (mixing and dilution). NO3− reduction was calculated to be responsible for 64% of the NO3− decline at 2 m, 28% at 2.5 and 47% at 3 m, respectively. Finally, by accounting for previous molecular and geochemical analysis at this site, and comparing the trajectories between Δδ18O: Δδ15N, we conclude that biological NO3− consumption at the two deeper and frequently saturated depths (2.5 and 3 m) can be attributed to heterotrophic denitrification. However, the Δδ18O: Δδ15N trajectory at the shallower, irregularly saturated site at 2 m shows a more complicated relationship best explained by the cyclic production of NO3− via aerobic oxidation, and consumption via NO3− reduction.