Sixteen endangered species including Schaus' swallowtail butterflies, smalltooth sawfish, manatees, and green and hawksbill sea turtles may be observed in the park.

[citation needed] In the early 20th century the islands became secluded destinations for wealthy Miamians who built getaway homes and social clubs.

The amphibious community of Stiltsville, established in the 1930s in the shoals of northern Biscayne Bay, took advantage of its remoteness from land to offer offshore gambling and alcohol during Prohibition.

The area remained undeveloped until the 1960s, when a series of proposals were made to develop the keys in the manner of Miami Beach, and to construct a deepwater seaport for bulk cargo, along with refinery and petrochemical facilities on the mainland shore of Biscayne Bay.

The park's western boundary is a fringe of property on the mainland, extending a few hundred meters inland between Cutler Ridge and Mangrove Point.

The park includes the southern portion of Biscayne Bay, with areas of thin sediment called "hardbottom", and vegetated seagrass meadows supporting turtlegrass and shoal grass.

[14] Native Americans were present in lower Florida 10,000 years ago, when ocean levels were low and Biscayne Bay was comparatively empty of water.

[16] The earliest evidence of human presence in Biscayne dates to about 2500 years before the present, with piles of conch and whelk shells left by the Glades culture.

[17] A site on Sands Key has yielded potsherds, worked shells and other artifacts indicating occupation from at latest 1000 CE to about 1650, after contact was made with Europeans.

[28] Few people lived in the park area until 1897, when Israel Lafayette Jones, an African-American property manager, bought Porgy Key for US$300 (equivalent to $11,000 in 2023).

Patrons included Warren G. Harding, Albert Fall, T. Coleman du Pont, Harvey Firestone, Jack Dempsey, Charles F. Kettering, Will Rogers and Frank Seiberling.

Clients guided by the Joneses through the 1940s and 1950s included then-senators John F. Kennedy, Lyndon Johnson, Richard Nixon, Herman Talmadge, and George Smathers.

[39] The town was incorporated to encourage Dade County to improve access to Elliott Key, which landowners viewed as a potential rival to Miami Beach.

Led by Lloyd Miller, the president of the local chapter of the Izaak Walton League, Miami Herald reporter Juanita Greene, and Art Marshall, the opponents of industrialization proposed the creation of a national park unit that would protect the reefs, islands and bay.

In 1968, when it appeared the area was about to become a national monument, Islandia supporters bulldozed a highway six lanes wide down the center of the island, destroying the forest for 7 miles (11 km).

[40] The oil-fired Turkey Point power stations were completed in 1967–68 and experienced immediate problems from the discharge of hot cooling water into Biscayne Bay, where the heat killed marine grasses.

Homestead Bayfront Park, still operated by Miami-Dade County just south of Convoy Point, established a "blacks-only" segregated beach for African-Americans at the present site of the Dante Fascell Visitor Center.

[49] The 1966 report noted the proposed park contained the best remaining areas of tropical forest in Florida and a rare combination of "terrestrial, marine and amphibious life," as well as significant recreational value.

The report found the most significant virtues of the potential park were "the clear, sparkling waters, marine life, and the submerged lands of Biscayne Bay and the Atlantic Ocean.

The hiring of a police chief in 1989 prompted questions from the National Park Service to the Dade County state attorney's office, headed by Janet Reno.

[79] Industrialist Mark C. Honeywell was a Cocolobo Club member who bought Boca Chita Key in 1937, expanding the facilities to include a small lighthouse.

[90] The sheltered open waters of the bay and the outlying chain of keys provide resting areas for migrating birds on their way between North American, the Caribbean islands, and South America.

The L-31E coastal storm surge levee inland of the park's western boundary has played a significant role in isolating former freshwater marshlands from their water sources.

All are fringed with mangroves, with subtropical vegetation and hardwood forests in the interiors, including gumbo limbo, mahogany, ironwood, torchwood and satinleaf.

Fish and Wildlife Service (USFWS) authorized a capture and captive breeding program for Schaus' swallowtail after only five of the butterflies were found by surveyors in the park, down from 35 in 2011, of a total surveyed Florida population of 41.

Areas farther offshore are protected within the Florida Keys National Marine Sanctuary, which extends eastward to a boundary corresponding to a depth of 300 fathoms (1,800 ft; 550 m).

[128] Green iguanas, cane toads, black rats, lionfish, fire ants, oscars and brown basilisk lizards are common in the park.

Sightings in Biscayne Bay at that time were believed to have been from home aquariums destroyed during the hurricane,[131] though the researcher who first proposed the theory has since retracted the assertion.

[142] On August 24, 1992, Hurricane Andrew came ashore just south of Miami, passing directly across Biscayne National Park with maximum sustained winds of 141 miles per hour (227 km/h), with gusts to 169 mph (272 km/h).

The inscription reads in part: On Monday, August 24, 1992, at 4:30 a.m., the eye wall of Hurricane Andrew passed over this point before striking Homestead and southern Miami-Dade County.