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Coral skeletons are made of aragonite, a very soluble form of calcium carbonate. The material is secreted as a way of disposing of excess ionic calcium.

Grazing and predation of fish and invertebrates causes portions of the coral skeletons to die, and these are immediately encrusted with algae, sponges, soft corals, or any of a myriad forms of small invertebrates. Over time, these too are grazed, silted over by coral sand, or out-competed by other organisms, and their remains become part of another compacted layer.

The lithification of coral rock is not well understood, but a fine-grained carbonate cement seems to form in the pores of the old coral, turning it into dense coral rock. This is thought perhaps to result from bacterial action.

The buildup of limestone on the reef is not a simple process of accumulation. It is a cycle just like the nutrient cycle. Scientists studying a 7-hectare reef in the Caribbean measured an annual production of 206 tons of calcium carbonate; they also measured an annual loss of 123 tons. The greatest part of this erosion was produced by boring sponges, and the rest by grazing fishes and echinoderms.