Hydrothermal activity in the crust results in the precipitation of large volumes of silica and often involves the formation of ore deposits, the shaping of geothermal systems, and recurring earthquakes. Pore fluid pressures fluctuate between lithostatic and hydrostatic, depending on seismic activity, and some models suggest the possibility of flash vaporization, given that fluid pressures can drop to the level of vapour at fault jogs during seismic slip. The phase changes of water could create extremely high supersaturations of silica, but the mechanisms of quartz vein formation under such extreme conditions remain unclear. Here we describe flash experiments conducted with silica-saturated solutions under conditions ranging from subcritical to supercritical. We found that amorphous silica is produced instantaneously as spherical nano- to micron-scale particles via nucleation and aggregation during the evaporation of water droplets. The nanoparticles are transformed to microcrystalline quartz very rapidly by dissolution and precipitation in hydrothermal solutions, with this process requiring less than one day under supercritical conditions because of the huge surface areas involved. We suggest that such short-lived silica nanoparticles have significant impacts on the dynamic changes in mechanical behaviour and hydrology of hydrothermal systems in volcanic areas.