Groundwater‐level changes after earthquakes provide insight into changes in hydrogeological properties such as permeability and pore pressure. Quantifying such changes, both their location and magnitude, is usually hindered by limited data. Using extensive high‐resolution water‐level monitoring records, we provide direct evidence of significant groundwater drawdown (4.74‐m maximum) over a 160‐km2 area along crustal ruptures after the Mw 7.0, 2016, Kumamoto earthquake. Approximately 106 m3 of water disappeared within 35 min after the main shock. The loss of water was not caused by static‐strain driven pore‐pressure decrease nor by releasing of water through structural pathways, but most likely by water transfer downwards through open cracks. Such changes may impact the security of water resources, the safety of underground waste repositories, and contaminant transport in seismically active areas.

Hydrogeological properties can change in response to large crustal earthquakes. In particular, permeability can increase leading to coseismic changes in groundwater level and flow. These processes, however, have not been well-characterized at regional scales because of the lack of datasets to describe water provenances before and after earthquakes. Here we use a large data set of water stable isotope ratios (n = 1150) to show that newly formed rupture systems crosscut surrounding mountain aquifers, leading to water release that causes groundwater levels to rise (~11 m) in down-gradient aquifers after the 2016 M w 7.0 Kumamoto earthquake. Neither vertical infiltration of soil water nor the upwelling of deep fluids was the major cause of the observed water level rise. As the Kumamoto setting is representative of volcanic aquifer systems at convergent margins where seismotectonic activity is common, our observations and proposed model should apply more broadly.

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