Abstract. The capillary fringe is a subsurface terrestrial-aquatic interface which 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 temporally discrete changes in nitrate concentrations lack the necessary resolution to partition between biotic or abiotic mechanisms. Here we take an experimental and mechanistic modeling approach to characterize the annual decline of nitrate (NO₃⁻) within floodplain sediments at Rifle, Colorado. At discrete sampling points during 2014 we measured NO₃⁻, ammonia (NH₄⁺), gaseous nitrous oxide (N₂O) and the corresponding isotopic composition of NO₃⁻. Coincident with an annual spring/summer excursion in groundwater elevation driven by snowmelt, we observed a rapid decline in NO₃⁻ concentrations at three depths (2, 2.5 and 3 m) below the ground surface. Isotopic measurements (i.e., 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 an initial dilution of NO₃⁻ within the well. Following extended saturation by groundwater at these depths we observed subsequent nitrate reduction. A simple Rayleigh model suggests depth-dependent variability in the importance of actively fractionating mechanisms (i.e., nitrate reduction) relative to non-fractionating mechanisms (mixing and dilution). Nitrate 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. Furthermore, we observed the highest concentrations of N₂O as groundwater saturated the 2 and 2.5 m depth, concomitant with enrichment of the δ¹⁵N_NO3 and δ¹⁸O_NO3. A mechanistic microbial model representing the diverse physiology of nitrifiers, facultative aerobes (including denitrifiers), and anammox bacteria indicates that the bulk of biological N loss within the capillary fringe is attributable to denitrifying heterotrophs. However, this relationship is dependent on the coupling between aerobic and anaerobic microbial guilds at the oxic-anoxic interface. Modeling insights also suggest that anammox might play a more prominent role in N loss under conditions where organic matter concentrations are low and rapidly depleted by aerobic heterotrophs prior to the rise of the water table.