The lands on which the park sits were originally inhabited by the Carijós and Tupiniquins Indians, who were displaced by the arrival of Portuguese settlers in the 1500s, though the Portuguese did not establish any significant settlements in the area.

In 1852, the Swiss consulate sent 15 families to settle on Superagüi Island, but the settlement failed to grow. Today, a few descendants of those families continue to live on park lands.

The park was declared a part of the Atlantic Forest Biosphere Reserve (or Mata Atlântica Biosphere Reserve), a UNESCO Biosphere Reserve, in 1991. It was declared a Brazilian national park in 1998. In 1999, the park was declared a UNESCO World Heritage Site.

The park is a marshy lowland area with miles of deserted beaches with dunes and coastal grasses waving in the sea breeze. Forests fill much of the land between the Atlantic Coastal beaches and the river banks and channel that separate the park from the mainland. The park includes a number of islands including Superagüi Island, Peças Island, Pinheiro Island, and Pinheirinho Island.

Each of the park's separate ecosystems has its own set of unique plants and animals. Ecosystems include the sandy coastal beaches, the mangroves and swamps along the river and channel, the dense inland tropical forests. Endangered species include the brown howler monkey and the red-tailed Amazons parrot. Other animals you are likely to see include alligators, monkeys, and perhaps some venomous snakes (including the jararaca and the coral snake).

Birdwatchers should plan to be in the park at dawn or dusk when flocks of parrots take flight. More than 2,000 parrots live on the island and leave each morning to seek food. The Baía dos Golfinhos on Ilha das Peças gets its name from the large number of dolphins that live in the isolated bay.

Vegetation includes ipês, jacaranda, figs, caxetas, and palm trees. Wildflowers found in the forest include several types of orchid.