In the 2011 off the Pacific coast of Tohoku Earthquake, groundwater pressure changes were observed in and around the Mizunami Underground Research Laboratory (MIU) in Central Japan, where two vertical shafts and horizontal research galleries are excavated in the granitic rock mass. Coseismic changes of groundwater pressure are believed to correspond to crustal dilation/contraction induced by earthquakes. In this study we calculated volumetric strain changes due to the Tohoku Earthquake based on previously reported fault slip models. The calculation indicates approximately 2 × 10−7 of dilational strain around the MIU. Based on the strain sensitivities calculated from tidal responses at the monitoring boreholes, the dilation corresponds to drawdowns of several tens of centimeters, and is almost the same as the drawdown observed in the boreholes at distances greater than 1 km from the MIU. In contrast, rapid elevation of groundwater pressures associated with the earthquake was observed in the boreholes within the 500 m vicinity of the MIU. The anomalous elevation is explained by a temporary recovery of the drawdown due to excavation of the shafts and a unique permeability increase induced by the coseismic dilation of heterogeneous local geological structures such as impervious faults controlling the hydrogeological environment.