Nitrate-nitrogen (NO3-N) contamination in groundwater has been worldwide concern, and especially it is a critical issue for the region depending on groundwater for water supply. Kumamoto city depends on only groundwater for all of water supply, however, lowering groundwater level and increasing NO3-N concentration have been revealed recently. In this study, the current situation of NO3-N contamination in the groundwater of Kumamoto city was investigated. Nitrate-nitrogen was detected in the range from 0.2 to 5.8 mg/l in the groundwater of deep wells at 22 points out of total 30 sampling points including drinking water resource. The NO3-N concentration was closely related to the location of wells and groundwater flow. The upward tendency in NO3-N concentration was recognized at a number of wells for recent 20 years, and it was considered due to the agricultural activity in the corresponding and their upstream areas.