In Tokamachi City, Niigata Prefecture, where Tertiary sedimentary rocks are distributed, excavation of the Mt. Nabetachiyama tunnel took a long time to complete due to the presence of a swelling mudstone zone. This swelling zone is distributed at a depth of 180m under the mud volcanoes. Geological and geographical surveys as well as electromagnetic surveys applying the Controlled Source Audio-frequency Magneto-Telluric Method (CSAMT), were carried out to clarify the geological structure under the mud volcanoes and the relationship between geographical features and the swelling zone. The laser scanner survey revealed that the geological structure around the topographic depression is intensely disturbed and the geological survey showed that the mud volcanoes and eruption points of groundwater and natural gas are located mainly along the outside edge of the geologically disturbed zone. This suggests that the area was active in the past due to the uplift and eruption of groundwater. The extremely low resistivity zone (ELR) at a depth of 400m with a diameter of 500m was detected below the geologically disturbed zone by the CSAMT survey. The ELR is estimated to correspond to a mud chamber filled with saline groundwater and mud, based on laboratory tests measuring the electrical properties of several rock samples obtained from the survey area. The low resistivity zone (LR) was also detected; it continues from the ELR to the mud volcano at the ground surface, indicating that saline groundwater, mud, and natural gas may be ascending via a concentric path to the mud volcanoes. On the basis of all the results obtained, it is interpreted that the swelling zone in the tunnel corresponds to the path of mobilized mud and saline groundwater in the fractured mudstone with abnormal pore water pressure.