Hydrogen is one of the most difficult elements to characterize in geological materials. Even at trace levels, hydrogen has a major impact on the properties of minerals, silicate melts, and fluids, and thus on the physical state of the mantle and crust. The investigation of H-bearing species in deep minerals, melts, and fluids is challenging because these phases can be strongly modified during transport to Earth’s surface. Furthermore, interpretation of experimental studies can be clouded by kinetic inhibitions and other artifacts. Nevertheless, recent improvements in analytical, experimental, and modeling methodologies have enabled advances in our understanding of how hydrogen is incorporated in the deep Earth, which is essential for constraining hydrogen cycling and storage through geologic time.