Intensive farming usually imply a degradation of groundwater resources worldwide. In particular, nitrate concentrations exceeding the 50 mg L−1 limit established for drinking water pose the human health at risk. Therefore, assessing the impact of farming on groundwater, in terms of space and time, is of fundamental importance for policy decision makers and land managers. This study was aimed at assessing the nitrate source and fate in groundwater by combining hydrogeochemical and isotopic tools. The study area is located in the coastal plain of Arborea (Italy), a nitrate vulnerable zone (NVZ) due to intensive farming and animal husbandry (28,000 bovine livestock units). This area represents Mediterranean environments where groundwater resources are of relevant importance.In order to assess the present level of groundwater contamination and evaluate temporal variations, 6 hydrogeochemical surveys were carried out bimonthly at 13 sampling sites located in an area of 6 km2. Additional samples were collected in specific surveys (82 water samples in total). The physical-chemical parameters, nitrogen species concentrations, major and minor components were determined, together with the boron, hydrogen, oxygen, nitrogen, and sulfur isotopic delta values.Results showed that groundwater samples were of meteoric origin, as indicated by the δ2H and δ18OH2O values. The groundwater showed near-neutral pH (6.8–7.9) and different values of redox potential (0.2 ÷ 0.5 V), dissolved oxygen (2 ÷ 6 mg L−1), electrical conductivity (0.8 ÷ 2.1 mS cm−1) and chemical composition (sodium-chloride ÷ calcium-bicarbonate). Nitrate was not homogeneously distributed in groundwater, being observed a large range of concentrations, from <1 up to 162 mg L−1. The above differences reflected the variability of groundwater circulation at small scale, which in turn controlled the interaction of water with different sediments (sands and/or clays). The shallow wells (about 5 m depth), screened in groundwater interacting mainly with sands, showed marked variations under the monitoring period, with nitrate peaks reflecting high leaching of nitrate in correspondence of fertilization and irrigation periods. The deeper wells (15–37 m depth) showed high to moderate nitrate when screened in sandy aquifer, whereas they had very low nitrate and relatively high ammonium (up to 1.8 mg L−1) when clay layers were intercepted.Trends of δ15N and δ18ONO3 values in the nitrate of shallow groundwater were related to the nitrate concentration observed over the monitored period. This dual isotope systematic showed a likely source of nitrate in groundwater from either manure or sewage. The δ11B signature coupled to δ15N values clearly identified the manure as the predominant source of nitrate in the shallow and deep groundwater at Arborea. Relative enrichments in heavy nitrogen coupled to high concentrations of nitrate in groundwater were mainly attributed to volatilization processes occurring during the storage of animal wastes prior to application on the soil. Mixing of groundwater with seawater was not recognized, whereas mixing between shallow and deep groundwater may have occurred locally.Natural attenuation of nitrate contamination was observed in the deep groundwater interacting with lagoon clays rich in organic matter. Heterotrophic denitrification processes were highlighted by relatively high δ15N, δ18ONO3, δ34S and δ18OSO4 values in association with low SO42−/Cl− and high HCO3−/SO42− molar ratios observed in the groundwater with low concentration of nitrate.Results of this study showed that site-specific investigations are required for designing the best practices aimed at preserving groundwater resources under Mediterranean conditions. The spreading of animal waste on soils affects groundwater systems and likely extends over long time, strongly depending on the time lag of nutrient transport from source areas to receptor wells. Therefore, adequate monitoring of groundwater quality is required in areas of intensive farming.