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 M_w 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.