Nitrogen is a vital nutrient helpful to plants and crop growth. However, among the leading causes of water resources pollution is the excess nitrogen from agricultural sources. In European Union countries, the Nitrates Directive has been approved to reduce this problem monitoring of water bodies with regard to nitrate concentrations, designation of Nitrate Vulnerable Zones (NVZs), and establishing codes of good agricultural practices and measures to prevent and reduce water pollution from nitrates. In light of this, we propose an integrated methodological approach to better manage a environmental issue as the perimeter of NVZs with the prospective that our approach could be used in the future by other member states representing a Best Practice in that direction. The methodology is based on data integration applied in a GIS environment. Different available data representing the knowledge of the territory were harmonised, systematised and georeferenced, in order to increase the environmental framework, preserve the contamination of the water resource and give indications on the measures to be implemented to apply in the best way possible the Nitrates Directive. Finally, it was also possible to overcome the infringement procedure in progress for Italy and the Puglia region and proceed to new designation of NVZs.