Hydrologic responses to earthquakes and their mechanisms have been widely studied. Some responses have been attributed to increases in the vertical permeability. However, basic questions remain: How do increases in the vertical permeability occur? How frequently do they occur? Is there a quantitative measure for detecting the occurrence of aquitard breaching? We try to answer these questions by examining data from a dense network of ∼50 monitoring stations of clustered wells in a sedimentary basin near the epicenter of the 1999 M7.6 Chi-Chi earthquake in western Taiwan. While most stations show evidence that confined aquifers remained confined after the earthquake, about 10% of the stations show evidence of coseismic breaching of aquitards, creating vertical permeability as high as that of aquifers. The water levels in wells without evidence of coseismic breaching of aquitards show tidal responses similar to that of a confined aquifer before and after the earthquake. Those wells with evidence of coseismic breaching of aquitards, on the other hand, show distinctly different postseismic tidal response. Furthermore, the postseismic tidal response of different aquifers became strikingly similar, suggesting that the aquifers became hydraulically connected and the connection was maintained many months thereafter. Breaching of aquitards by large earthquakes has significant implications for a number of societal issues such as the safety of water resources, the security of underground waste repositories, and the production of oil and gas. The method demonstrated here may be used for detecting the occurrence of aquitard breaching by large earthquakes in other seismically active areas.