Nanopores are ubiquitous in porous geologic media and may account for >90% of total mineral surface areas. Surface chemistry, ion sorption, and the related geochemical reactions within nanopores can be significantly modified by a nanometer-scale space confinement. As the pore size is reduced to a few nanometers, the difference between surface acidity constants (ΔpK = pK2 − pK1) decreases, giving rise to a higher surface charge density on a nanopore surface than that on an unconfined mineral-water interface. The change in surface acidity constants results in a shift of ion sorption edges and enhances ion sorption on nanopore surfaces. Also, the water activity in a nanopore is greatly reduced, thus increasing the tendency for inner sphere complexation and mineral precipitation. All these effects combine to preferentially enrich trace elements in nanopores, as observed in both field and laboratory studies. The work reported here sheds new light on such fundamental geochemical issues as the irreversibility of ion sorption and desorption, the bioavailability of subsurface contaminants, and the enrichment of trace metals in ore deposits, as well as the kinetics of mineral dissolution and/or precipitation.