Hernando de Escalante Fontaneda related in the 16th century that a sailor from the Bay of Biscay called the Viscayno or Biscayno had lived on the lower east coast of Florida for a while after being shipwrecked, and a 17th-century map shows a Cayo de Biscainhos, the probable origin of the name for Key Biscayne.

The British, during their occupation of Florida (1763–1783), called the lagoon "Cape River", "Dartmouth Sound", and "Sandwich gulph".

[3] Biscayne Bay is a semi- or subtropical lagoon extending most of the length of Miami-Dade County, from North Miami Beach to the upper Florida Keys.

The lagoon, from Dumfoundling Bay to the Arsenicker Keys, has a surface area of about 572 square kilometres (221 sq mi).

[1][2][4][5][6] The eastern rim of the lagoon is based on an ancient coral reef which existed along the southeastern edge of the Florida Platform about 100,000 years ago.

The dead reef became fossilized, forming the Key Largo Limestone (commonly called "coral rock").

Key Largo Limestone underlies the Eastern edge of the barrier islands and the shoals (Safety Valve) along the northern and middle part of the lagoon.

[1][7] The limestone bottom of the lagoon is overlain by 1.2 to 4.6 metres (3.9 to 15.1 ft) of sand, carbonate mud, and coral rubble sediments.

More than 40% of the area of North Bay had either been dredged or filled to form artificial islands, and more than half of the remaining lagoon bottom is barren.

Turbidity is high in North Bay due to erosion from spoil islands and banks, and the lack of vegetation on the lagoon bottom.

Dodge Island, across the main ship channel to the south of the MacArthur Causeway, was enlarged in the 1960s when the Port of Miami was moved there from the mainland north of Bayfront Park.

Fresh water sources for Central Bay include the Coral Gables Waterway and Snapper Creek.

Central Bay has been adversely affected primarily by bulkheading, urban runoff discharged by canals, and the loss of natural fresh water flow.

Mark C. Honeywell bought the key in 1937, and built a large retreat on the island, including a 65-foot (20 m) tall faux lighthouse.

[15] South Bay is the least affected by human activities, although it also suffers from the loss of natural fresh water flow.

The term "safety valve" was applied to the tidal flats by Ralph Munroe, who argued against building a causeway and bridges connecting Key Biscayne to the Ragged Keys and beyond on the grounds that such construction would block the free outflow of storm surges from the bay across the flats to the ocean.

The transportation of sand southward along the Atlantic Coast of Florida by longshore drift ends in the area of the Safety Valve.

[18])[19][20][21] Stiltsville is a collection of buildings on pilings on several sand flats at the northern end of the Safety Valve.

Ralph Munroe noted in the late 19th century that potable water could be pumped from one of those bay bottom springs.

Human bones, teeth, and artifacts that are almost 11,000 years old have been found at the Cutler Fossil Site, a sinkhole that is now a couple of kilometers from the bay.

[28][29] The opening of Government Cut in 1905 separated Fisher Island from Miami Beach and slightly shortened the barrier spit.

Modification of the flow of fresh water through waterways, and the opening of Government Cut and the Baker's Haulover Inlet during the 20th century increased the salinity of the lagoon.

The first bridge across Biscayne Bay was the 2.5-mile (4.0 km) wooden Collins Bridge built in 1912 by John S. Collins and his son-in-law Thomas Pancoast, who formed the Miami Beach Improvement Corporation; financing was provided by Carl G. Fisher and the Miami banker brothers John N. Lummus and James E.

[37] In 1929, a third causeway crossed Biscayne Bay at Normandy Isle, which developer Henri Levy had created several years earlier by dredging and filling the south half of Meade Island.

The Card Sound Bridge connects the mainland in the Homestead, Florida area to the northern part of Key Largo.

Bill Baggs Cape Florida State Park is located on the southern part of Key Biscayne.

Black Point, Crandon, Haulover, Homestead Bayfront and Matheson Hammock parks have public marinas.

The preserve was created by the Florida Legislature in 1974, and then included all of Biscayne Bay from the Oleta River to the southern end of Card Sound.

The sanctuary includes all of the lagoon from a line running from Cape Florida to Matheson Hammock County Park south to the Card Sound Bridge and causeway.

[48] The sea level at Virginia Key has been rising at an average rate of 2.97 millimetres (0.117 in) a year from 1931 to 2020, equivalent to 0.97 feet (0.30 m) a century.