After the United States acquired Florida from Spain in 1819, military planners recognized the Dry Tortugas as a strategic chokepoint controlling the Straits of Florida and the Gulf of Mexico. Construction of Fort Jefferson began on Garden Key, and by 1860 the work was half complete. The fort is massive: the largest brick masonry structure in the Western Hemisphere, with walls eight feet thick and gun emplacements designed to hold 450 cannons. The labor force consisted largely of enslaved people hired from their owners in Key West; between 1847 and 1860, roughly seventeen percent of Key West's enslaved population was leased to the Army Corps of Engineers for the project. White laborers, mostly Irish immigrants, also worked the site. The use of enslaved labor ended in 1863, and the 82nd United States Colored Infantry was stationed at the fort near the end of the Civil War. The fortress remained in Union hands throughout the conflict, but its most famous role was as a prison.

In 1865, Dr. Samuel Mudd set the broken leg of a man who arrived at his Maryland farm in the middle of the night. That man was John Wilkes Booth, fleeing after assassinating President Abraham Lincoln. Mudd was convicted of conspiracy by a military commission, narrowly escaping the death sentence by a single vote, and was shipped to Fort Jefferson in irons along with three other Lincoln assassination conspirators. The fort was already a grim place: isolated, sweltering, plagued by mosquitoes and disease. In 1867, yellow fever swept through the garrison. When the post surgeon died, Mudd stepped in, treating soldiers and prisoners alike through the epidemic. His courage earned him a petition for clemency from the fort's officers and soldiers, and President Andrew Johnson pardoned him in 1869. Mudd's cell is preserved today, a small room where one of the strangest chapters in American history played out against a backdrop of coral and salt water.

The waters around the Dry Tortugas are a graveyard. Shipwrecks dating from the seventeenth century litter the reefs, victims of hurricanes, shallow coral, and the treacherous currents of the Florida Straits. The most famous is the Nuestra Senora de Atocha, a Spanish galleon driven onto a reef by a hurricane on September 6, 1622. Treasure hunter Mel Fisher discovered the wreck on July 20, 1985, after a sixteen-year search. The recovered cache was valued at an estimated $450 million: 40 tons of gold and silver, 114,000 silver pieces of eight, Colombian emeralds, gold artifacts, and 1,000 silver ingots. Fisher's company also found the Atocha's sister galleon, the Santa Margarita, lost the same year, and the remains of the Henrietta Marie, a slave ship lost in 1700. In 1742, the crew of a wrecked British vessel lived on Garden Key for 56 days, fought a battle with a Spanish sloop, and then sailed to Jamaica in improvised boats.

The Dry Tortugas host the only nesting colonies of sooty terns, brown noddies, magnificent frigatebirds, and masked boobies in the contiguous United States. The park's official bird list counts 299 species. Each spring, particularly in April, the islands become a waystation for migrating warblers, and birders can tally over 100 species in a single day. Many exhausted migrants land inside the parade grounds of Fort Jefferson itself, where they rest at close range among the brick arches. Bush Key, just meters from Garden Key, is closed to visitors from February through September to protect tens of thousands of nesting sooty terns and brown noddies. John James Audubon visited the Tortugas in 1832; Louis Agassiz came in 1858. From 1903 to 1939, the Carnegie Institution operated a marine biology laboratory on Loggerhead Key that became the best-equipped tropical marine station in the world, hosting over 150 researchers.

The Dry Tortugas are not fixed. There are nominally seven islands, but there have been as many as eleven over the past two centuries, and some of them vanish. Middle Key disappears for weeks or months at a time beneath the tides, only to resurface. Bird Key, once the site of Union soldiers' graves, disappeared entirely in 1935. Southwest Key, North Key, and Northeast Key were all gone by 1875. The three largest islands, Loggerhead Key, Garden Key, and Bush Key, account for 93 percent of the total land area, which itself shifts with every storm. The underlying geology is ancient: the Florida Keys are the surface expression of a carbonate platform that has been accumulating sediments since the Early Cretaceous, over 100 million years ago. The coral reefs here were once the most extensive in the Florida Keys, but the cold wave of January 1977 wiped out 96 percent of shallow-water branching coral, leaving rubble fields that the park is still recovering from. Despite this, the Dry Tortugas reefs remain the least disturbed in the Florida Keys, a fragile wilderness at the end of the American road.