Mission Bay Park is home to many rare and endangered species, including the California least tern. A program goes into effect every April through August to protect the endangered California least tern at four of its nesting sites in Mission Bay Park. The California least tern is is a federally-listed endangered subspecies, and the death of a least tern chick severely reduces chances for the bird's survival. The roaming of predators on site prevents adult least terns from nesting.
In a multi-agency effort, that includes the City of San Diego Park and Recreation Department, the U.S. Department of Fish and Wildlife Service, the California Department of Fish and Wildlife, and the Wildlife Services Program of the U.S. Department of Agriculture; professionals from the wildlife program carry out the humane trapping of least tern predators who come to least tern nesting sites. This includes skunks, opossums, and feral cats and dogs, believed to be former pets who were abandoned by their owners. Sites are located on North Fiesta Island, Mariner's Point, Stoney Point, and a small island called "Government Island" used by the Federal Aviation Agency.
Anyone exercising a dog in Mission Bay Park should adhere to the posted leash laws, and should consider leashing the dog in off-leash areas as well during the least tern season.
Other birds that can be seen in Mission Bay Park are the great blue heron, the osprey, mallards, avocets, black-necked stilts and the Belding's savannah sparrow.