Japan Atomic Energy Agency has undertaken the Mizunami Underground Research Laboratory (MIU) Project at Gifu Pref., central Japan. The aims of the project are to establish methodologies for investigation, analysis, and assessment of the deep geological environment, and to develop engineering techniques for deep-underground applications. The MIU consists of two vertical shafts and a number of horizontal tunnels connecting the two shafts. In this study, hydrochemical properties were monitored continuously to evaluate the hydrochemical changes during the MIU construction. The study demonstrated that groundwater salinity changed in relation to the variation of groundwater-flow conditions as a result of the shaft construction. In particular, "up-coning" of the salinity profile was observed at the bottom of the shafts owing to the upward movement of deeper groundwater. The intensity of up-coning was irregular, and depended on the hydrogeological heterogeneity of the groundwater system. Although pH rose to around 12 due to interaction with the concrete lining the shafts and with the grout injected into the adjacent host rock, it decreased to below 10 in less than 2 years. The redox condition remained reducing, which is considered to be controlled by Fe2+/Fe(OH)3(am) and/or SO4 2−/FeS2 couples. These findings can be summarized in a conceptual model.