Nitrate (NO3−) loss from agriculture to shallow groundwater and transferral to sensitive aquatic ecosystems is of global concern. Denitrifying bioreactor technology, where a solid carbon (C) reactive media intercepts contaminated groundwater, has been successfully used to convert NO3− to di-nitrogen (N2) gas. One of the challenges of groundwater remediation research is how to track denitrification potential spatially and temporally within reactive media and subsoil. First, using δ15N/δ18O isotopes, eight wells were divided into indicative transformational processes of ‘nitrification’ or ‘denitrification’ wells. Then, using N2/argon (Ar) ratios these wells were divided into ‘low denitrification potential’ or high denitrification potential’ categories. Secondly, using falling head tests, the saturated hydraulic conductivity (Ksat) in each well was estimated, creating two groups of ‘slow’ (0.06 m day−1) and ‘fast’ (0.13 m day−1) wells, respectively. Thirdly, two ‘low denitrification potential’ wells (one fast and one slow) with high NO3− concentration were amended with woodchip to enhance denitrification. Water samples were retrieved from all wells using a low flow syringe to avoid de-gassing and analysed for N2/Ar ratio using membrane inlet mass spectrometry. Results showed that there was good agreement between isotope and chemical (N2/Ar ratio and dissolved organic C (DOC)) and physio-chemical (dissolved oxygen, temperature, conductivity and pH) parameters. To explain the spatial and temporal distribution of NO3− and other parameters on site, the development of predictive models using the available datasets for this field site was examined for NO3−, Cl−, N2/Ar and DOC. Initial statistical analysis was directed towards the testing of the effect of woodchip amendment. The analysis was formulated as a repeated measures analysis of the factorial structure for treatment and time. Nitrate concentrations were related to Ksat and water level (p < 0.0001 and p = 0.02, respectively), but did not respond to woodchip addition (p = 0.09). This non-destructive technique allows elucidation of denitrification potential over time and could be used in denitrifying bioreactor technology to assess denitrification hotspots in reactive media, while developing a NO3− spatial and temporal predictive model for bioreactor site specific conditions.