Metal ions, toxic or potentially toxic to biota and human beings, can be immobilized by sorption onto the mineral surfaces in soils and sediments. This article briefly explains theories regarding the chemical properties of mineral surfaces to sorb metal ions and processes of extended X-ray absorption fine structure (EXAFS) analysis for sorption study, and reviews atomic-scale findings on metal sorption on mineral surfaces. The theoretical understanding on the chemistry of mineral surfaces and metal sorption is fundamental to the proper analysis of the atomic-scale spectroscopy to determine the sorption phases. Atomic-scale findings on metal sorption phases discussed here include co-precipitation, ternary complexation, aging effects, and desorption possibilities, as well as outer-sphere complexation, inner-sphere complexation, and surface precipitation.