For a better understanding of the effects of regional groundwater management for different land-use types on nitrogen content in groundwater, we investigated the Miyakonojo River Basin in south of Japan where the Nitrate Directive Plan has been in practice since 2004. For this purpose, we used nitrogen concentrations from 420 wells between 2000 and 2017 together with 8 different land-use categorizations. The data were analyzed using self-organizing maps (SOM) and results showed that forest recharge areas have lowest mean nitrogen concentrations of about 2.9 mg/L. Urban areas displayed a mean nitrogen concentration of about 4.4 mg/L. Agricultural land such as paddy fields had a mean nitrogen concentration of about 5.1 mg/L. Groundwater discharge and residential areas had mean groundwater nitrogen concentrations of 8.2 and 7.1 mg/L, respectively. Intensive agricultural land-use and wastewater discharge from urban areas caused the main groundwater nitrogen contamination in these areas. About 70% of the wells had a decreasing trend of groundwater nitrogen concentration (p < 0.05, p ≥ 0.05) during the period 2009–2017. About 20% of the wells displayed a trend reversal from 2000–2008 (increasing) to 2009–2017 (decreasing). In general, the Nitrate Directive Plan appears to have had positive effects for mitigating groundwater nitrogen problems. However, 30% of the wells still do not display a decreasing trend and some wells exceed maximum permissive level for drinking water. Thus, management needs to continue to improve groundwater conditions regarding nitrogen content.