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In human-impacted rivers, nutrient pollution has the potential to disrupt biodiversity organisation and ecosystem functioning, prompting calls for effective monitoring and management. Pollutants, together with natural variations, can modify the isotopic signature of aquatic organisms. Accordingly, we explored the potential of isotopic variations as an indicator of drainage basin influences on river food webs. We assessed stable N and C isotopes within six food webs along a river affected by multiple pollution sources. CORINE land cover maps and Digital Elevation Models (DEMs) were also applied to understand the impact on surface waters of anthropogenic pressures affecting the catchment. N isotopic signatures of taxa fell in association with ammonium inputs from agriculture, indicating that nitrogen pollution was related to synthetic fertilizers. Isotopic variations were consistent across trophic levels, highlighting site-specific communities and identifying taxa exposed to pollutants. This allowed us to locate point sources of disturbance, suggesting that food web structure plays a key role in pollutant compartmentalisation along the river. Thematic maps and DEMs helped understand how the anthropogenic impact on river biota is mediated by hydro-geomorphology. Thus, the integration of site-scale analyses of stable isotopes and land use represents a promising research pathway for explorative nutrient pollution monitoring in human-impacted rivers.