The hydrological system within Earth's crust is divided into the permeable zone and the underlying, much less permeable zone. In this study, we investigated the solubility and precipitation kinetics of silica in water under the conditions of the Kakkonda geothermal field, Japan, where well WD-1a penetrates the boundary between the hydrothermal convection zone and the heat conduction zone. We found that quartz solubility has a local minimum at the depth of the hydrological boundary, at ~3100-m depth (380 °C and 24 MPa), in the case of either hydrostatic conditions or fluid pressure increase above hydrostatic at deeper levels. The hydrothermal experiments reveal that rapid quartz precipitation occurs via nucleation when fluids are brought from the liquid region to the supercritical region. The preferential precipitation of quartz at a specific depth plays a significant role in forming and sustaining the permeable-impermeable boundary in the crust.