Abstract We determined thermal equations of state of hydrated stishovite and CaCl2‐type SiO2 up to 100 GPa and 3,000 K to assess the gravitational stability of hydrated stishovite and basaltic crust in the lower mantle. Using machine‐learning based atomistic simulations, we examined three hydrogen dissolution mechanisms: hydrogarnet‐type, interstitial H2O, and coupled Al3+ + H+ substitution. Hydrogen dissolution lowers SiO2 densities throughout the lower mantle and reduces bulk sound velocities at its upper part. Hydrated basaltic crust with 1–4 wt% H2O in SiO2 remains 1%–2.4% denser than the mantle and can sink to the lowermost mantle, potentially forming water‐rich reservoirs influencing seismic and electrical anomalies at depths. Stishovite with 0.3–2.2 wt% H2O is neutrally buoyant at 730–800 km, supporting its role as a source of low shear‐wave velocity layers beneath North America, Japan, and the European Alps subduction regions. These results provide new insights into water storage and transport in the deep mantle.