Deep underground, magma (molten rock) heats water, which is less dense than cold water, so it tends to rise toward the surface. The hot water can carry dissolved minerals into fissures and cracks in the Earth's crust. When minerals are dissolved in a liquid, scientists say that the minerals are in solution. Eventually, the water cools and the materials in the water crystallize out of solution in their new location, and the resulting minerals look different from the surrounding rocks. Hydrothermal comes from the Greek words for water and heat; these structures are called hydrothermal veins because they resemble the blood vessels in the bodies of animals. Many ores of economically important metals, such as lead, zinc, copper, and gold, are found in these veins.

Inside a mineral, atoms arrange themselves into a specific, repeating pattern called a crystal lattice or crystal structure. The smallest three-dimensional arrangement within the lattice is called a "unit cell," which is duplicated over and over again symmetrically. At the level of the everyday world, minerals that are growing without outside interference tend to form crystals that resemble their underlying crystal structures. Scientists call that kind of general, typical appearance a "crystal habit." Of course, conditions that existed during a mineral's formation or crystal growth may change its habit, but geologists still find this attribute to be a useful tool for identifying minerals. Scientists use more than three dozen adjectives to describe crystal habits. For example, natrolite and rutile can be acicular, or needlelike; quartz often forms hexagonal prisms; pyrite and halite typically crystallize as cubes; and mica is foliated or lamellar (layered).