[4] Guanabara Bay was first encountered by Europeans on January 1, 1502, when Portuguese explorers Gaspar de Lemos and Gonçalo Coelho[5] arrived on its shores.

After they were expelled by Portuguese military expeditions in 1563, the colonial government built fortifications in several points of Guanabara Bay, rendering it almost impregnable against a naval attack from the sea.

They were the Santa Cruz, São João, Lajes and Villegaignon forts, forming a fearsome crossfire rectangle of big naval guns.

Underwater exploration in the bay was disallowed by the Brazilian government in 1985 amid a dispute with American writer and treasure hunter Robert Marx, who claimed to have found evidence of a Roman shipwreck.

[7] Carl Feagans tells of 16 amphorae made for antiques-lover Americo Santarelli in 1960 or 1961, all 16 of which deliberately sunk in the bay for them to acquire the look of ancient artefacts covered in barnacles and corals; 4 of the 16 original amphorae were subsequently recovered, leaving 12 scattered about the bay, where two were found by lobster divers in 1974.

Guanabara Bay's once rich and diversified ecosystem has suffered extensive damage in recent decades, particularly along its mangrove areas.

The most recent was in 2000 when a leaking Petrobras underwater pipeline released 1,300,000 litres (340,000 US gal) of oil into the bay, destroying large swaths of the mangrove ecosystem.

[11] In June 2014, Dutch windsurfer and former Olympic and world champion Dorian van Rijsselberghe made an urgent appeal to government and industry in the Netherlands to collaborate in cleaning up the bay, together with the Plastic Soup Foundation.