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San Francisco Bay in California has been served by ferries of all types for over 150 years. Although the construction of the Golden Gate Bridge and the San Francisco-Oakland Bay Bridge led to the decline in the importance of most ferries, some are still in use today for both commuters and tourists.

One of the earliest ferry routes ran between San Francisco and Oakland on what was called the "creek route". The name derived from the Oakland landing site located on what is today called the Oakland Estuary, an inlet of San Francisco Bay. The estuary, which in the 1800s included what is today's Lake Merritt, was the "creek".

The Southern Pacific Company's Bay City ferry plies the waters of San Francisco Bay in the late 19th century.

The first railroad ferries on San Francisco Bay were established by the Central Pacific Railroad and were an integral part of the Transcontinental Railroad. The earliest railroad ferries ran from Alameda when it was still a peninsula. Another ferry pier was established at Oakland Point, the Oakland Long Wharf. These railroad ferries mostly carried passengers, not trains, although there was some ferrying of freight cars to San Francisco. When the Central Pacific re-routed the Sacramento to Oakland segment of the Transcontinental Railroad in 1876, a ferry across the Carquinez Strait was established, and the world's largest ferryboat, the Solano was built (later joined by a sister ferry, the slightly larger Contra Costa), to serve the crossing. This railroad ferry actually carried whole trains. These ferries became part of the Southern Pacific Railroad when it assumed many of the facilities of its affiliate, the Central Pacific.

The Key System transit company established its own ferry service in 1903 between the Ferry Building in San Francisco and its own pier and wharf ("mole") on the Oakland shoreline, located just south of what is today the eastern approach to the San Francisco-Oakland Bay Bridge.

In the 1920s, the Southern Pacific Railroad established a subsidiary, the Golden Gate Ferries, to carry automobiles on three routes: the Golden Gate between the Hyde Street Pier in San Francisco and Sausalito in Marin County; San Francisco Bay between the Hyde Street Pier and the Berkeley Pier; and San Francisco Bay between San Francisco and the Oakland Pier. These ferries ceased operation shortly after the Golden Gate and Bay Bridges were opened.

The largest ferry system on San Francisco Bay today is operated by Golden Gate Transit. Modern high speed ferryboats of this commuter system run between the Ferry Building in San Francisco and landings in Sausalito and Larkspur in Marin County.

Other commuter ferries run from the city of Alameda, Jack London Square in Oakland and Vallejo to the Ferry Building in San Francisco.

Tourist ferries run from Fisherman's Wharf to Alcatraz Island, and from Sausalito to Angel Island.

The Santa Fe's San Pablo ferry travels across San Francisco Bay in the early 20th century.

• Bay City (Southern Pacific)
• Berkeley (Southern Pacific)
• Contra Costa (Central Pacific/Southern Pacific)
• Eureka (Northwestern Pacific/Southern Pacific)
• Fresno (Southern Pacific)
• Hayward (Key System)
• Newark (Southern Pacific)
• Oakland (Southern Pacific)
• Ocean Wave (Santa Fe)
• Peralta (Key System)
• Sacramento (Southern Pacific)
• San Leandro (Key System/Southern Pacific)
• San Pablo (Santa Fe)
• San Pedro (Santa Fe)
• Santa Clara (Southern Pacific)
• Solano (Central Pacific/Southern Pacific)

• Del Norte (Golden Gate)
• Mare Island (Vallejo Baylink)
• Mendocino (Golden Gate)
• San Francisco (Golden Gate)
• Solano (Vallejo Baylink)
• Sonoma (Golden Gate)
• Vallejo (Vallejo Baylink)

• San Francisco Bay : A Pictorial Maritime History, by John Haskell Kemble, Bonanza Books (1957, 1978).

• San Francisco Bay Ferryboats, by George H. Harlan, Howell-North Books (1967).

• San Francisco Bay Ferryboats

• Golden Gate Transit