Nitrate contamination is one of the main risks for groundwater in agricultural areas. The evaluation of the effect of agricultural practices on groundwater nitrate concentration, especially in highly sensitive areas, is crucial for a correct land planning, and a good agronomic intervention scheduling. Aim of this paper is to map the probability to exceed nitrate regulatory threshold applying a non-parametric geostatistical approach, the Indicator Kriging (IK). A study in the Fucino Plain (Abruzzo, Central Italy), characterized by highly profitable intensive agriculture with mainly irrigated horticultural and short rotation crops, was carried out. The Plain has a shallow and controlled groundwater table, and channels draining the surplus water during winter. Water samples were collected monthly from piezometers and analysed for nitrate. IK provided a model of spatial uncertainty, representing the probability that the threshold of 50 mg/L fixed by the European Nitrate Directive is exceeded, and results were transferred into a GIS. Maps obtained for each month showed how the probability to exceed the threshold changes during an average year. The methodology can provide an effective operative tool to support decision-makers for the identification and the designation of nitrate vulnerable zones.