The numerous ship wrecks that occurred along the southeast coast of Florida from Key Biscayne to the Dry Tortugas was a cause for concern. Between the late 1840s and the late 1850s, more than 500 ships were wrecked on the Florida Reef. The Assistant United States Coast Surveyor reported that in the period from 1845 through 1849, almost one million (United States) dollars worth of vessels and cargoes were lost on the reef. In 1846, US Congress appropriated $23,000 to rebuild the Cape Florida lighthouse and work was completed in 1847. In 1849 the United States Board of Engineers conducted a preliminary survey of the coast of Florida. In a report written by Lieutenant Colonel Robert E. Lee, the Board recommended that Key Biscayne be made a military reservation, and the United States Secretary of War so ordered in March 1849. Later that year, the United States Army Corps of Topographical Engineers set up a camp with an astronomical/magnetic station to serve as a datum base for a survey of the Florida Keys and the Great Florida Reef. To learn more about the Great Florida Reef, Alexander Bache invited Louis Agassiz to study it. The U.S. Coast Survey sent Agassiz to Key Biscayne in 1851. He wrote a detailed report for Bache on the reefs stretching from Key Biscayne to the Marquesas Keys. The triangulation survey was conducted by the U.S. Coast Survey with men detailed from the U.S. Army and U.S. Navy. Approximately forty men were based at Cape Florida working on the survey when Alexander Dallas Bache, Superintendent of the U.S. Coast Survey, went to Key Biscayne in 1855 to take charge of it. The survey eventually covered Key Biscayne, Biscayne Bay, the Florida Keys from south of Key Biscayne to the Marquesas Keys, and Florida Bay from the Keys to Cape Sable. In 1861, Confederate militants sabotaged the lighthouse so that it could not guide Union sailors during the blockade of ConfederateFlorida. The lighthouse was repaired and re-lit again in 1866. In 1878 the Cape Florida Light was replaced by the Fowey Rocks Light, seven miles (11 km) southeast of Cape Florida. From 1888 to 1893, the Cape Florida lighthouse was leased by the United States Secretary of the Treasury for a total of US$1.00 (20 cents per annum) to the Biscayne Bay Yacht Club for use as its headquarters. It was listed as the southernmost yacht club in the United States, and the tallest in the world. After the lease expired, the yacht club moved to Coconut Grove, where it continues. In 1898, in response to the growing tension with Spain over Cuba, which led to the Spanish–American War, the Cape Florida lighthouse was briefly made U.S. Signal Station Number Four. It was one of 36 along the U.S. East Coast and Gulf Coast from Maine to Texas. The Signal Stations were established to provide an early warning of any approach of the Spanish fleet. The north base marker for Key Biscayne was discovered in 1970 as workers were clearing land. It was at first mistaken as a gravestone for someone named A. D. Bache. The survey base marker at Cape Florida ended up under water, as the south end of the island eroded. It could be seen at low tide as late as 1913. In 1988 the Cape Florida base marker was recovered from under water and installed near the Cape Florida lighthouse.
Key Biscayne, although named a “key”, is not geologically part of the Florida Keys, but is a barrier island composed of sand eroded from the Appalachian Mountains, carried to the coast by rivers and then moved along the coast from the north by coastal currents. There is no hard bedrock near the surface of the island, only layers of weak “shelly sandstone” to depths of 100 feet (30 m) or more. The coastal transport of sand southward ends at Key Biscayne. In the 1850s Louis Agassiz noted that “[s]outh of Cape Florida no more silicacious sand is to be seen.” (The beaches in the Florida Keys, by contrast, consist primarily of finely pulverized shells.) Geologists believe that the island emerged around 2000 BCE, soon after the sea level stopped rising, as the sand built up to form new barrier islands on the southern Florida coast.
Key Biscayne is elongated in the north-south direction, tapering to a point at each end. It is approximately 5 miles (8.0 km) long and 1 to 2 miles (1.6 to 3.2 km) wide. The northern end of the island is separated from another barrier island, Virginia Key, by Bear Cut. The southern end of the island is Cape Florida. The Cape Florida Channel separates the island from the Safety Valve, an expanse of shallow flats cut by tidal channels that extends southward about 9 miles (14 km) to the Ragged Keys, at the northern end of the Florida Keys. Only Soldier Key, approximately 200 by 100 yards (183 by 9 m) wide, lies between Key Biscayne and the Ragged Keys. The Cape Florida Channel (ten to eleven feet [three to three-and-a-half meters] deep in 1849) and Bear Cut (four feet [a little more than one meter] deep in 1849) are the deepest natural channels into Biscayne Bay. They provided the only access for ocean-going vessels to Biscayne Bay until artificial channels were dredged starting early in the 20th century. In 1849 the island had a fine sandy beach on the east side, and mangroves and lagoons on the west side. The average elevation of the island is less than five feet (1.5 m) above sea level.