The stable nitrogen and oxygen isotopic tracers play an important role in determining the causes of groundwater nitrate contamination, natural attenuation capacity, and their extension on a regional scale. However, it is not well known how these pollution characteristics change in response to long-term changes in land use patterns and environmental countermeasures continuously applied, considering that groundwater flows with long residence time. This may be due to the fact that the acquisition of isotope datasets so far has been generally transient, and there has been a lack of datasets to examine the temporal changes on a long-term scale. To test a potential utility of these isotopic indicators in detecting long-term shift in the pollution cause, we collected 243 groundwater samples from regional aquifers in the Kumamoto region to assess isotopic changes in 10 years and analyzed the data with long-term social databases such as estimated nitrogen load and water quality for the past 60 years (1960–2020), for a period comparable to the groundwater residence time. Our analytical results showed that in the recent 10 years (2009–2019) the percentage of groundwater samples mainly affected by chemical fertilizers and livestock waste decreased from 25.0% to 16.2% and increased from 16.1% to 41.3%, respectively, based on our proposed nitrogen isotopic thresholds. This result indicates that the major cause of pollution tends to shift from the application of chemical fertilizers to the leakage of animal waste. The agricultural census data showing gradual long-term shift in the major nitrogen load from application of chemical fertilizers to livestock farming corresponds to the results from isotopic analysis. Furthermore, the long-term nitrate concentration trend analysis revealed that the impact of chemical fertilizer influence decreased for several reasons, whereas that of leakage of animal waste became dominant and has caused the current environmental problems mainly in the north-central part of the study region. The distribution of denitrification has not changed during the past decade. The results of this study suggest that the main factors of nitrate contamination in groundwater can change gradually over time. This study demonstrates that monitoring of nitrogen and oxygen isotopic indicators at regular intervals with long-term continuous social datasets is effective for determining up-to-date conditions and changing processes of groundwater quality, which provide important base information to build critical guidelines for local environmental measure discipline.
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