Although the ecozone represents only 2% of Canada, it embraces a wide variety of critical terrestrial, freshwater, and marine environments. Kelp and seaweed along rocky coasts provide shelter and food for various marine communities of mussels and crab. The Scotian Shelf off Nova Scotia is one of the most productive offshore areas in the ecozone. Low-lying beaches and tidal flats of the Upper Bay of Fundy and the southern Gulf of St. Lawrence are dominated by burrowing crustaceans. The Gulf is well-known for its scallop, mackerel, groundfish, and herring fisheries. Seals, dolphins, porpoises and Black Guillemots are among the higher predators within the ecozone. Both seal- and whale-watching are popular tourist attractions.

Rivers draining the area are vital for the commercially important Atlantic Salmon and other ocean fish that return to inland streams to spawn. Brook Trout, Gaspereau, Halibut, and Bass are highly valued by recreational and commercial fishers.

Lakes and shaded waterways within forests supply habitat for herons, loons, and freshwater ducks, while osprey and eagles nest in tall trees. Canada Goose, Blue-winged Teal, Ring-necked Duck, and 31 other bird species breed exclusively in the unique freshwater habitats of the Atlantic region. Tens of thousands of shore and migratory birds feed on crustaceans in the tidal mudflats of the Bay of Fundy. With productive seas and substantial coastal estuaries, the Atlantic Maritime Ecozone is often referred to as “an international crossroads for seabirds.

Much of the ecozone's wildlife is dependent on forest ecosystems. Terrestrial mammals include Black Bear, Bobcat, Snowshoe Hare, Northern Flying Squirrel, and White-tailed Deer. Large moose herds concentrate in various regions, especially in the heart of the Chics-Chocs mountains of the Gaspé Peninsula. Wolves, Mink, and the occasional Lynx also reside in the ecozone.

Alteration and loss of habitat from human activities are the greatest threat to wildlife. Fragmented landscapes and species decline can be attributed to logging, agriculture, overfishing, and urbanization. The Grey Whale has disappeared from the Atlantic after centuries of hunting. The endangered status of the Acadian Whitefish is the result of overfishing and water quality degradation from acid rain and other contaminants. The threatened Roseate Tern's feathers were exploited by the fashion trade of the 19th and early 20th centuries. Today, the species is challenged by expanding Herring Gull populations preying on its eggs and chicks.

Many initiatives have been taken to preserve the ecozone's unique fauna. Provincial regulations and protected areas help maintain species and habitat. Machias Seal Island, a migratory bird sanctuary in the Bay of Fundy, is home to the only colonies of the Atlantic Puffin and Razorbill in New Brunswick. Several species also seek refuge in the ecozone's six national parks. The threatened Blanding's Turtle population, for example, is almost exclusively confined to acidic waters and peaty soils within Kejimkujik National Park.