[5][6] Lieutenant James Cook first landed at Kurnell, on the southern banks of Botany Bay, in what is now Silver Beach, on Sunday 29 April 1770, when navigating his way up the east coast of Australia on his ship, HMS Endeavour.

[8] Cook's log for 6 May 1770 records "The great quantity of these sort of fish found in this place occasioned my giving it the name of Stingrays Harbour".

However, in the journal prepared later from his log, Cook wrote instead: (sic) "The great quantity of plants Mr. Banks and Dr. Solander found in this place occasioned my giving it the name of Botanist Botany Bay".

[citation needed] Eighteen years later, Governor Arthur Phillip sailed the armed tender HMS Supply into the bay on 18 January 1788.

In 1789, Captain John Hunter surveyed Botany Bay after returning from the Cape of Good Hope, trading for grain.

The western shore of Botany Bay remained in its virgin state for almost fifty years after the initial settlement of Sydney Town.

After World War II the mouth of the Cooks River was moved two kilometres west to make way for the airport extension.

A second container terminal was completed during the 1980s and bulk liquid storage facilities are located on the northern and southern edge of the bay.

Despite its relative isolation, the southern shore of the bay is dominated by an unusual mixture of pristine national park and heavy industrial use that includes Sydney Desalination Plant, the Caltex Fuel Terminal, sewer treatment, and historical sand mining facilities.

[12] On the southern side of the bay a section of water has been fenced off under the authority of the NSW National Parks & Wildlife Service at Towra Point for environmental conservation purposes.

[14] The world's largest population of weedy sea dragon ever surveyed is found at the 'Steps' dive site, on the Kurnell side of the Botany Bay National Park.

The eastern blue groper[15] is the state fish of New South Wales; it is very tame and is commonly found following divers along the shoreline of Botany Bay.