The fate of nitrate transported across groundwater-surface water interfaces has been intensively studied in recent decades. The interfaces between aquifers and rivers or lakes have been identified as biogeochemical hotspots with steep redox gradients. However, a detailed understanding of the spatial heterogeneity and potential temporal variability of these hotspots, and the consequences for nitrogen processing, is still hindered by a paucity of adequate measurement techniques. A novel methodology is presented here, using Diffusive Equilibrium in Thin-film (DET) gels as high-spatial-resolution passive-samplers of δ15NNO3 and δ18ONO3 to investigate nitrogen cycling. Fractionation of δ15NNO3 and δ18ONO3 during diffusion of nitrate through the DET gel was determined using varying equilibrium times and nitrate concentrations. This demonstrated that nitrate isotopes of δ15NNO3 and δ18ONO3 do not fractionate when sampled with a DET gel. δ15NNO3 values from the DET gels ranged between 2.3 ± 0.2 and 2.7 ± 0.3‰ for a NO3– stock solution value of 2.7 ± 0.4‰, and δ18ONO3 values ranged between 18.3 ± 1.0 and 21.5 ± 0.8‰ for a NO3– stock solution of 19.7 ± 0.9‰. Nitrate recovery and isotope values were independent of equilibrium time and nitrate concentration. Additionally, an in situ study showed that nitrate concentration and isotopes provide unique, high-resolution data that enable improved understanding of nitrogen cycling in freshwater sediments.