Nitrate concentration in groundwater has frequently been linked to non-point pollution. At the same time the existence of intensive agriculture and extremely intensive livestock activity increases the potential for nitrate pollution in shallow groundwater. Nitrate used in agriculture could cause adverse effects on human and animal health. In order to evaluate the groundwater nitrate pollution, and how it might evolve in time, it is essential to develop control systems and to improve policies and incentives aimed at controlling the amount of nitrate entering downstream water systems. The province of Caserta in southern Italy is characterized by high levels of animal manure loading. A comparison between manure nitrogen production and nitrate concentration in groundwater was carried out in this area, using geostatistical tools and spatial statistics. The results show a discrepancy between modelling of nitrate leaching and monitoring of the groundwater and, moreover, no spatial correlation between nitrogen production in livestock farms and nitrate concentration in groundwater, suggesting that producers are not following the regulatory procedures for the agronomic use of manure. The methodology developed in this paper could be applied also in other regions in which European Union fertilization plans are not adequately followed.