Various tribes of Native Americans inhabited the Keys before the first European explorers arrived. Middens and other remains are located throughout the islands documenting their earliest human occupation. After Key West was settled, "Conch" families moved up the Keys to establish small farming and fishing communities. In the mid-1800s, the Russell family homesteaded Umbrella Key, Windley’s earlier name. The Russell family lived on the land until it was sold to the Florida East Coast Railway in 1908 for $852.80. From that time, until the final completion of the Overseas Railroad, the quarries along the tract were used to supply thousands of tons of fill for the railbed and the bridge approaches.

The railroad was completed in 1912 and the quarries and Windley Key Station continued to serve in many ways. Local trains stopped daily to deliver much needed fresh water from the mainland and pick up mail and passengers. On return trips, shipments of polished "keystone" were railed back to the mainland. This keystone, a decorative building stone, can be seen on several buildings throughout the United States including the St. Louis Post Office, an altar in a New York City chapel and many other locations. Local examples include the Alison Fahrer Environmental Education Center at Windley Key and the Hurricane Monument located in the center of Islamorada. The quarry was active into the 1960s and today stands as a preserved geological treasure. The clean cuts of the quarry machinery reveal the perfectly preserved fossilized specimens of a variety of ancient coral animals. The park offers a rare opportunity to professional geologists and curious visitors to compare the living corals of today with their fossilized ancestors. The limestone cuts also reveal the thin layer of soil that supports the abundant variety of botanical life that thrives in the subtropical environment of the Keys.