Opalinus Clay is chosen as host rock for the deep geological disposal of nuclear waste in Switzerland and is also being considered in Germany. The underlying Staffelegg Formation comprises potentially water-bearing layers. To investigate the hydrogeological setting of these two formations at the Swiss Rock Laboratory in Mont Terri two bore holes have been drilled in the framework of the HS-Experiment (Hydrogeological Survey). The 58 m long BHS-1 starts in the Lower Shaly facies of the Opalinus Clay, crossects the entire Staffelegg formation and ends in the Triassic Klettgau formation. The shorter BHS-2 provides additional data from the carbonate-rich sandy facies and Lower Shaly facies of the Opalinus Clay. The presented data publication provides geochemical, mineralogical and petrophysical parameters of rocks, pore water and (dissolved) gases from these two drillings. In the following the main measured parameter are listed: geochemical composition of bulk rock and single minerals, isotopic data of carbonates and S isotopes of bulk rock, cation exchange, analyses of organic compounds, bulk rock and clay mineralogy, bulk density, porosity, water content, noble gases, pore water composition, composition and isotopes of dissolved gases and water isotopes.