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Salinization and nitrate pollution are generally ascertained as the main issues affecting coastal aquifers worldwide. In arid zones, where agricultural activities also result in soil salinization, both phenomena tend to co-exist and synergically contribute to alter groundwater quality, with severe negative impacts on human populations and natural ecosystems’ wellbeing. It becomes therefore necessary to understand if and to what extent integrated hydrogeochemical tools can help in distinguishing among possible different salinization and nitrate contamination origins, in order to provide adequate science-based support to local development and environmental protection. The alluvial plain of Bou-Areg (North Morocco) extends over about 190 km(2) and is separated from the Mediterranean Sea by the coastal Lagoon of Nador. Its surface is covered for more than 60% by agricultural activities, although the region has been recently concerned by urban population increase and tourismexpansion. All these activities mainly rely on groundwater exploitation and at the same time are the main causes of both aquifer and lagoon water quality degradation. For this reason, it was chosen as a case study representative of the typical situation of coastal aquifers in arid zones worldwide, where a clear identification of salinization and pollution sources is fundamental for the implementation of locally oriented remedies and long-term management strategies. Results of a hydrogeochemical investigation performed between 2009 and 2011 show that the Bou-Areg aquifer presents high salinity (often exceeding 100 mg/L in TDS) due to both natural and anthropogenic processes. The area is also impacted by nitrate contamination, with concentrations generally exceeding the WHO statutory limits for drinking water (50 mg/L) and reaching up to about 300 mg/L, in both the rural and urban/peri-urban areas. The isotopic composition of dissolved nitrates (delta N-15(NO3) and delta O-18(NO)) was used to constrain pollution drivers. The results indicate two main origins for human-induced pollution: (i) manure and septic effluents, especially in urban areas, and (ii) synthetic fertilizers in agricultural areas. In the latter, delta N-15-enriched values highlight a mixture of those sources, possibly related to unbalanced fertilization and agricultural return flow. Boron isotopes (delta B-11) were hence studied to further distinguish the nitrate origin in the presence of multiple sources and mixing processes. The results indicate that in the study area, the high geochemical background for B and Cl, associated to the complex waterrock interaction processes, limit the application of the coupled delta B-11 and delta N-15 isotopic systematics to the detection of sources of groundwater pollution. In fact, despite the exceedingly high nitrate contents, the depleted delta B-11 values that characterize synthetic fertilizers and sewage leakages could not be detected. Therefore, even if in saline groundwater the anthropogenic contribution has a negligible effect in terms of salinity input, with both sewage and irrigation water not very charged, the associated nitrate content fuels up water-rock interaction processes, eventually leading to a mineralization increase.