Nitrates are the most common chemical pollutant of groundwater in agricultural and suburban areas. Croatia must comply with the Nitrate Directive (91/676/EEC) whose aim is to reduce water pollution by nitrates originating from agriculture and to prevent further pollution. Podravina and Prigorje are the areas with a relatively high degree of agricultural activity. Therefore, the aim of this study was, by monitoring nitrates, to determine the distribution of nitrates in two different areas, Podravina and Prigorje (Croatia), to determine sources of contamination as well as annual and seasonal trends. The nitrate concentrations were measured in 30 wells (N = 382 samples) in Prigorje and in 19 wells (N = 174 samples) in Podravina from 2002 to 2007. In Podravina, the nitrate content was 24.9 mg/l and 6% of the samples were above the maximum available value (MAV), and in Prigorje the content was 53.9 mg/l and 38% of the samples above MAV. The wells were classified as correct, occasionally incorrect and incorrect. In the group of occasionally incorrect and incorrect wells, the point sources were within 10 m of the well. There is no statistically significant difference over the years or seasons within the year, but the interaction between locations and years was significant. Nitrate concentrations' trend was not significant during the monitoring. These results are a prerequisite for the adjustment of Croatian standards to those of the EU and will contribute to the implementation of the Nitrate Directive and the Directives on Environmental Protection in Croatia and the EU.