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.