The bay remains as a home port of major assets, including several aircraft carriers of the United States Pacific Fleet.

[8] Formerly known as Commercial Basin and housing much of San Diego's sport and commercial fishing fleet, the small cove in the southern lee of Shelter Island was renamed in 1994 to America's Cup Harbor, in honor of the 1995 America's Cup races held in San Diego.

It featured flights over San Diego Bay by more than 200 historic naval aircraft,[17] and concluded with a flyover by the air wing from the U.S.S.

[18] The western border of the bay is protected from the Pacific Ocean by a long, narrow strip of land called Silver Strand.

The salt ponds, Sweetwater Marsh, and other areas of the bay are included in the San Diego National Wildlife Refuge Complex.

[20] It is an important stop on the Pacific Flyway for migrating birds, and it supports numerous endangered and threatened species of plants and animals.

[23] Sources of pollution in the bay include storm-water runoff and marine waste from commercial and military shipping and shipbuilding.

The city of San Diego has spent millions of dollars trying to clean up this pollution, particularly at the section of the eastern shoreline referred to as the Shipyards Sediment Site.

[24] In 2009 the city and the San Diego Unified Port Authority filed suit against several major shipping companies to recoup some of the cost of those remediation efforts.

In 2014 the city reached an agreement with the San Diego Regional Water Control Board to pay a fine of nearly $1 million for storm-water violations.

[24] In 2015, the city and the Port filed suit against Monsanto, whose products containing polychlorinated biphenyls (PCBs) are blamed for pollution of the bay and tidelands.

[25] The California Office of Environmental Health Hazard Assessment (OEHHA) has developed a safe eating advisory for fish caught in the bay based on levels of mercury or PCBs found in local species.

It is a special government entity created by the state legislature in 1962, for which revenue consists of tariffs and rents paid by district tenants.