The Chesapeake Bay is home to numerous fauna that either migrate to the Bay at some point during the year or live there year-round. There are over 300 species of fish and numerous shellfish and crab species. Some of these include the Atlantic menhaden, striped bass, American eel, eastern oyster, Atlantic horseshoe crab, and the blue crab.
Birds include ospreys, great blue herons, bald eagles, and peregrine falcons, the last two of which were threatened by DDT; their numbers plummeted but have risen in recent years. The piping plover is a near threatened species that inhabits the wetlands.
Larger fish such as Atlantic sturgeon, varieties of sharks, and stingrays visit the Chesapeake Bay. The waters of the Chesapeake Bay have been regarded as one of the most important nursery areas for sharks along the east coast. Megafaunas such as bull sharks, tiger sharks, scalloped hammerhead sharks, and basking sharks and manta rays are also known to visit. Smaller species of sharks and stingrays that are known to be regular to occasional residents in the bay include the smooth dogfish, spiny dogfish, cownose ray, and bonnethead.
Bottlenose dolphins are known to live seasonally/yearly in the Bay. There have been unconfirmed sightings of humpback whales in recent years. Endangered North Atlantic right whale and fin, and minke and sei whales have also been sighted within and in the vicinity of the Bay.
A male manatee visited the Bay several times between 1994 and 2011, even though the area is north of the species normal range. The manatee, recognizable due to distinct markings on its body, was nicknamed "Chessie" after a legendary sea monster that was allegedly sighted in the Bay during the 20th century. The same manatee has been spotted as far north as Rhode Island, and was the first manatee known to travel so far north. Other manatees are occasionally seen in the Bay and its tributaries, which contain sea grasses that are part of the manatees diet.
Loggerhead turtles are known to visit the Bay.
The Chesapeake Bay is also home to a diverse flora, both land and aquatic. Common submerged aquatic vegetation includes eelgrass and widgeon grass. A report in 2011 suggested that information on underwater grasses would be released, because "submerged grasses provide food and habitat for a number of species, adding oxygen to the water and improving water clarity." Other vegetation that makes its home in other parts of the Bay are wild rice, various trees like the red maple, loblolly pine and bald cypress, and spartina grass and phragmites. Invasive plants have taken a significant foothold in the Bay. Plants such as Phragmites, Purple loosestrife and Japanese stiltgrass have established high levels of permanency in Chesapeake wetlands. Additionally, plants such as Brazilian waterweed, native to South America, have spread to most continents with the help of aquarium owners, who often dump the contents of their aquariums into nearby lakes and streams. It is highly invasive and has the potential to flourish in the low-salinity tidal waters of the Chesapeake Bay. Dense stands of Brazilian waterweed can restrict water movement, trap sediment and affect water quality. Various local K-12 schools in the Maryland and Virginia region often have programs that cultivate native bay grasses and plant them in the Bay.