The dissolution-precipitation of minerals is an important geochemical process, which affects the spatial and temporal state of a geothermal system. Fractures sealed by mineral precipitation are commonly observed at the permeable-impermeable boundary in deep drilling wells that encountered higher pore-fluid pressure. This indicates that the mineral deposition plays a crucial role on the formation of the bottom of the hydrothermal convection zone in geothermal fields. In this study, quartz solubility is calculated along the axis of the deep drilling wells as the key parameter to understand the nature of the permeable-impermeable boundary. The mineralization around the permeable-impermeable boundary has been explained by the pressure change of the upward deep-crustal fluid from lithostatic to hydrostatic across the permeable-impermeable boundary. The calculation in this study shows that the state of the downward fluid changes from liquid to vapor or to a supercritical phase due to the high temperature gradient, and that it also causes a drastic decrease in quartz solubility, and enhances quartz precipitation at the permeable-impermeable boundary. The mixing of CO2 or NaCl fluid as deep-crustal gas/fluid with meteoric water also contributes to the local change in quartz solubility. In the geothermal field, the permeable-impermeable boundary has a high possibility of being formed and controlled by the significant mineral deposition which could occur from both upward and downward crustal fluid. The precipitation of minerals should be considered for the development of the deep geothermal resources.