During the Silurian Period 425 million years ago, when much of North America was covered by a shallow, tropical sea, reefs grew in the area now occupied by Wisconsin and Illinois.  A reef is a structure built by organisms that rises above the surrounding seafloor. Reefs are built in warm, shallow seawater in the tropics and subtropics. They occur only in waters that are relatively free of suspended, land-derived sediment, which allows sunlight to penetrate to the reef surface, permitting photosynthetic organisms to live.

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The Thornton Reef developed from coral growth centers on the bottom of the ancient Silurian Sea.  The reefs were covered with a diverse array of strange marine invertebrates, most of which are now extinct.  Corals, crinoids, and shelled invertebrates flourished.  The Thornton reef was home to sea lilies, animals resembling horseshoe crabs, and ancient ancestors of squids and octopuses up to ten feet long.  A species of Pentamerid brachiopods (Kirkidium knightii) was common and could  grow to sizes of over 10 cm.  A thickened beak area served as a weight to stabilize the shell in the sediment, and there was no fixed attachment. They often lived as clumps of individuals.  Today, Pentamerid brachiopod fossils are easy to find on the floor of the quarry.

During the Silurian Age, the coral took in sea-water and processed out the lime. The lime deposits from the coral hardened and produced limestone. When the coral died, it stayed on top of the limestone and became part of the formation. Young coral then laid eggs on the limestone structure and began the process all over again. The result was coral and other dead sea life encased in layers and layers of limestone.