Groundwater under industrial sites is characterised by heterogeneous chemical mixtures, making it difficult to assess the fate and transport of individual contaminants. Quantifying the in-situ biological removal (attenuation) of nitrogen (N) is particularly difficult due to its reactivity and ubiquity. Here a multi-isotope approach is developed to distinguish N sources and sinks within groundwater affected by complex industrial pollution. Samples were collected from 70 wells across the two aquifers underlying a historic industrial area in Belgium. Below the industrial site the groundwater contained up to 1000 mg N l⁻¹ ammonium (NH₄⁺) and 300 mg N l⁻¹ nitrate (NO₃⁻), while downgradient concentrations decreased to ∼1 mg l⁻¹ DIN ([DIN] = [NH₄⁺-N]+NO₃^--N]+NO₂^--N]. Mean δ¹⁵N-DIN increased from ∼2‰ to +20‰ over this flow path, broadly confirming that biological N attenuation drove the measured concentration decrease. Multi-variate analysis of water chemistry identified two distinct NH₄⁺ sources (δ¹⁵N-NH₄⁺ from −14‰ and +5‰) within the contaminated zone of both aquifers. Nitrate dual isotopes co-varied (δ¹⁵N: −3‰ – +60‰; δ¹⁸O: 0‰ – +50‰) within the range expected for coupled nitrification and denitrification of the identified sources. The fact that δ¹⁵N-NO₂⁻ values were 50‰–20‰ less than δ¹⁵N-NH₄⁺ values in the majority of wells confirmed that nitrification controlled N turnover across the site. However, the fact that δ¹⁵N-NO₂⁻ was greater than δ¹⁵N-NH₄⁺ in wells with the highest [NH₄⁺] shows that an autotrophic NO₂⁻ reduction pathway (anaerobic NH₄⁺ oxidation or nitrifier-denitrification) drove N attenuation closest to the contaminant plume. This direct empirical evidence that both autotrophic and heterotrophic biogeochemical processes drive N attenuation in contaminated aquifers demonstrates the power of multiple N isotopes to untangle N cycling in highly complex systems.