Limestone often contains variable amounts of silica in the form of chert or flint, as well as varying amounts of clay, silt and sand as disseminations, nodules, or layers within the rock.

The primary source of the calcite in limestone is most commonly marine organisms. These organisms secrete shells that settle out of the water column and are deposited on ocean floors as pelagic ooze or alternatively is conglomerated in a coral reef (see lysocline for information on calcite dissolution). Secondary calcite may also be deposited by supersaturated meteoric waters (groundwater that precipitates the material in caves). This produces speleothems such as stalagmites and stalactites. Another form taken by calcite is that of oolites (oolitic limestone) which can be recognized by its granular appearance. Limestone makes up about 10% of the total volume of all sedimentary rocks.

Calcite can be either dissolved by groundwater or precipitated by groundwater, depending on several factors including the water temperature, pH, and dissolved ion concentrations. Calcite exhibits an unusual characteristic called retrograde solubility in which it becomes less soluble in water as the temperature increases.
When conditions are right for precipitation, calcite forms mineral coatings that cement the existing rock grains together or it can fill fractures.

Karst topography and caves develop in carbonate rocks due to their solubility in dilute acidic groundwater. Cooling groundwater or mixing of different groundwaters will also create conditions suitable for cave formation.

Coastal limestones are often eroded by organisms which bore into the rock by various means. This process is known as bioerosion. It is most common in the tropics, and it is known throughout the fossil record (see Taylor and Wilson, 2003).

Pure limestone is almost white. Because of impurities, such as clay, sand, organic remains, iron oxide and other materials, many limestones exhibit different colors, especially on weathered surfaces.

Limestone may be crystalline, clastic, granular, or massive, depending on the method of formation. Crystals of calcite, quartz, dolomite or barite may line small cavities in the rock. Folk and Dunham classifications are used to describe limestones more precisely.

Travertine is a banded, compact variety of limestone formed along streams, particularly where there are waterfalls and around hot or cold springs. Calcium carbonate is deposited where evaporation of the water leaves a solution that is supersaturated with chemical constituents of calcite. Tufa, a porous or cellular variety of travertine, is found near waterfalls. Coquina is a poorly consolidated limestone composed of pieces of coral or shells.

During regional metamorphism that occurs during the mountain building process (orogeny) limestone recrystallizes into marble.

Limestone is a parent material of Mollisol soil group.

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