Kumamoto city and its neighboring municipalities, which is more than 1,000 km
2 in area and have almost 1 million people, are considered a mesoscale region. This region is a special area in Japan and in the world because of the fact that all drinking water demand by most of its population is met using only groundwater. However, recently, nitrate-nitrogen (NO
3-N) contamination has been a source of concern. The goal of this study is to examine the groundwater contamination by NO
3-N in this area and to determine the factors of nitrogen load. NO
3-N concentration was higher than 4 mg·L
-1 in many wells, it was even higher than 10 mg·L
-1 in some wells in upstream areas of groundwater. In addition, most groundwater samples showed an upward trend in NO
3-N concentration in recent years. The Geographical Information System (GIS) technique using agricultural census data revealed that nitrogen emission from domestic animal waste significantly increased in the upstream areas of groundwater, which was coincident with the NO
3-N contamination of groundwater. The nitrogen stable isotope ratios (δ
15N) of NO
3-N in groundwater were relatively high (9.6 to 15) in most of the wells, and especially higher (10<) in the upstream areas of groundwater. From these results, domestic animals waste and the application of organic fertilizers were identified by the effective combination of the GIS technique and δ
15N analysis as the main contributors to NO
3-N contamination.
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