Groundwater flow velocity as well as conductive and convective heat fluxes were estimated using temperature profile data from a 1000 m–deep borehole in the central part of the Izu-Oshima volcano, Japan. Two depth intervals below groundwater level with upward groundwater flow patterns were examined assuming a one-dimensional vertical steady flow. The groundwater velocity and total heat flux were estimated to be 5.0–5.4×10-10 m/s and 0.54–0.59 W/m2, respectively, for the basement layer (Formation 4). For the shallower layer (Formation 2), both the upward velocity and heat flux were higher, indicating greater contributions of convective mass and heat transfer compared to those in the deeper layer. Furthermore, assuming that the upward flow was buoyancy-driven, vertical permeabilities of 2.8–5.1×10-15 and 1.7–3.1×10-16 m2 , respectively, were estimated for Formations 2 and 4. The temperature patterns of the lava-dominant region (Formation 3), sandwiched between Formations 2 and 4, suggested the occurrence of lateral cooler groundwater inflow in fractures. These results were used for understanding a hydrothermal system beneath the volcano. The total heat flux estimated for Formation 4 (0.54–0.59 W/m2) was nearly three times higher than the conductive heat flux in the northwestern coastal area, suggesting a higher heat supply below the central part of the volcano. A hydrothermal free convection system was inferred in Formations 2 and 3. In Formation 2, buoyancy-driven upward flow was enhanced because of the heat below and the higher permeability. Cooler groundwater was laterally supplied in lava fractures in Formation 3 to compensate for the mass loss by the upward flow at the bottom of Formation 2.