San Francisco Bay is a shallow, productive estuary through which water draining from approximately forty percent of California, flowing in the Sacramento and San Joaquin rivers from the Sierra Nevada mountains, enters the Pacific Ocean. Technically, both rivers flow into Suisun Bay, which flows through the Carquinez Strait to meet with the Napa River at the entrance to San Pablo Bay, which connects at its south end to San Francisco Bay, although the entire group of interconnected bays are often referred to as "San Francisco Bay."

San Francisco Bay is a mecca for sailors, due to consistent strong easterly winds (Beaufort force 6 is common on summer afternoons) and protection from large open ocean swells. Yachting and yacht racing are popular pastimes and the San Francisco Bay Area is home to many of the world's top sailors.

Despite its urban and industrial character, San Francisco Bay and the Sacramento-San Joaquin Delta remain perhaps California's most important ecological habitats. California's Dungeness crab, Pacific halibut, and Pacific salmon fisheries rely on the bay as a nursery. The few remaining salt marshes now represent most of California's remaining salt marsh, supporting a number of endangered species and providing key ecosystem services such as filtering pollutants and sediments from the rivers. Most famously, the bay is a key link in the Pacific Flyway. Millions of waterfowl annually use the bay shallows as a refuge. Two endangered species of birds are found here: the California least tern and the California clapper rail. Exposed bay muds provide important feeding areas for shorebirds, but underlying layers of bay mud pose geological hazards for structures near many parts of the bay perimeter.

In 1972 the U.S. government created the Golden Gate National Recreation Area. It now includes some 30,226 hectares (74,689 acres) of land and water embracing city, county, state, and federal parklands in three counties. Far larger than the city of San Francisco, the recreation area is the largest urban national park in the world. Nearly 20 million visitors visit the park each year, making it one of the most popular federal recreational facilities. Among its attractions are Muir Woods National Monument, which is located north of the Golden Gate on the coast and features old-growth redwood trees; Alcatraz Island, which is an abandoned federal penitentiary that once held gangster Al Capone; and many beaches.

Dillon Beach is located near the mouth of Tomales Bay.

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