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Detailed studies on pollutants genesis, path and transformation are needed in agricultural catchments facing coastal areas. Here, loss of nutrients should be minimized in order to protect valuable aquatic ecosystems from eutrophication phenomena. A soil system N budget was calculated for a lowland coastal area, the Po di Volano basin (Po River Delta, Northern Italy), characterized by extremely flat topography and fine soil texture and bordering a network of lagoon ecosystems. Main features of this area are the scarce relevance of livestock farming, the intense agriculture, mainly sustained by chemical fertilizers, and the developed network of artificial canals with long water residence time. Average nitrogen input exceeds output terms by ~60 kg N ha(-1) year(-1), a relatively small amount if compared to sub-basins of the same hydrological system. Analysis of dissolved inorganic nitrogen in groundwater suggests limited vertical loss and no accumulation of this element, while a nitrogen mass balance in surface waters indicates a net and significant removal within the watershed. Our data provide multiple evidences of efficient control of the nitrogen excess in this geographical area and we speculate that denitrification in soil and in the secondary drainage system performs this ecosystemic function. Additionally, the significant difference between nitrogen input and nitrogen output loads associated to the irrigation system, which is fed by the N-rich Po River, suggests that this basin metabolizes part of the nitrogen excess produced upstream. The traditionally absent livestock farming practices and consequent low use of manure as fertilizer pose the risk of excess soil mineralization and progressive loss of denitrification capacity in this area.