The Gulf is one of the two primary nesting sites of the critically endangered hawksbill sea turtle in the eastern Pacific.

[1][2] [3] There are a variety of habitat types on the margins of the Gulf of Fonseca - mangrove forests, mudflats, sandy beaches and rocky cliffs.

The mangroves tend to line the lagoons, bays, and flat lowlands.

Associated species include Avicennia bicolor, and black mangrove (Avicennia germinans)[1] The mangrove habitats of the Gulf of Fonseca in Honduras, with those of La Unión Bay in El Salvador as well as the Estero Real Delta and Apacunca Plains of Nicaragua, have been designated an Important Bird Area (IBA) by BirdLife International because they support significant populations of reddish egrets, red knots, semipalmated sandpipers, elegant terns lesser ground-cuckoos, Pacific screech-owls, Hoffmann's woodpeckers, orange-fronted parakeets, Nutting's flycatchers, white-throated magpie-jays and banded wrens.

[7][8][9] Officially protected areas in the ecoregion include: There are also nature reserves along the inlets at Chismuyo Bay, San Lorenzo Bay, Las Iguanas and Punta Condega, Jicarito, and San Bernardo.