The waters over the continental shelf of the Northwest Atlantic are famous for their prolific communities of marine mammals, birds, and fish. It is home for part of the year to the now-famous endangered Northern Cod. Twenty-two species of whale and six species of seal occur in the ecozone. Pods of Humpback, Sei, Fin, and Minke Whales are most likely to be spotted, along with the occasional Blue Whale. Sperm Whales can be found further offshore. Orcas, porpoises and dolphins also occur, but are not common. Millions of Harp Seals live along the coasts. There is debate as to whether Harp Seals share some of the blame for the decline of the cod stocks.

Steep, rocky cliffs and thousands of islands provide ideal habitat for some of the largest seabird colonies in the world. Concentrations occur on the Gannet Islands off the southern Labrador coast and the Funk Islands off Newfoundland's northeast coast. Large colonies of Puffins, Petrels, Cormorants, Thick-billed Murres, and several varieties of gull also nest in the Gulf of St. Lawrence on Anticosti Island, Bonaventure Island, and the Magdalen Islands.