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This study presented the first attempt to detect precursory changes in groundwater level before the 2016 Kumamoto Earthquake. This detection was achieved by accurately determining the relationship between long-term groundwater level fluctuation and crustal deformation over 16 years through analysis of groundwater level time-series data acquired at 17 sites within the study area. Here, we show that the observed groundwater levels were lower than the modelled levels in aquifers composed of porous strata (Togawa lava and part of the pre-Aso volcanic rocks), and that there were larger differences until 2014, which diminished until the occurrence of the Kumamoto Earthquake. The initial reduction in the modelled groundwater level and the latter recovery were most likely caused by crustal strain relaxation associated with the large 2011 earthquake off the Pacific coast of Tohoku (Mw 9.0) and the strain accumulation prior to the 2016 Kumamoto Earthquake. [ABSTRACT FROM AUTHOR]