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This study aimed at clarifying the relationship between the dynamics of land use/land cover (LULC) changes and decline in the groundwater levels, and specifying an LULC category strongly affecting such decline in a Quaternary sedimentary basin. Groundwater level data recorded at 26 observation wells for a 14-year period in the Kumamoto Plain, central Kyushu, southwest Japan, were used for the analysis. The general trends of LULC were detected by a satellite image classification technique and surface spline method, which highlighted the decreases in groundwater-recharge materials. As the next step, those trends of groundwater levels that were closely correlated with rainfall were removed from the level data set, and the resultant residual component levels were applied to co-kriging analysis with LULC categories. Co-kriging provided a detailed map of groundwater level variability. Furthermore, we propose a method, prediction of residual of groundwater level (PWL), to infer future residual groundwater levels from the supposed LULC pattern by co-kriging-based modeling. PWL was demonstrated to be effective because it clearly represented the decrease and increase in negative residual level areas, depending on the extent of rice fields in the past and in predicted future distribution scenarios.