Golden Gate Ferry has a fleet of four catamarans and three monohull vessels. All ferries are wheelchair accessible. The catamarans can carry 30 bicycles, and the monohull vessels can carry 150 bicycles. All ferries have restrooms and on-board refreshments, including a full bar.
The monohull vessels are named MS Marin, MS San Francisco, and MS Sonoma. Marin can carry 750 passengers, and San Francisco and Sonoma can carry 630 passengers each. They were purchased from Philip F. Spaulding & Associates in San Diego in 1976–1977. They were originally powered by gas turbine water jets but were converted to diesel engine propeller drives in 1983–1985. More efficient diesel engines were installed in 2001–2002. The Marin was refurbished from November 2006 to July 2007.
The catamarans are named MV Del Norte, MV Golden Gate, MV Mendocino, and MV Napa. Del Norte has a capacity of 400 passengers while the other three vessels have a capacity of 450 passengers. The 1998-built Del Norte and 2001-built Mendocino were built for Golden Gate Ferry to allow faster and more frequent service than the monohull ferries. Napa (formerly Snohomish) and Golden Gate (formerly Chinook) were purchased from Washington State Ferries in January 2009.
In late 2018, Golden Gate Ferry reached an agreement to lease MV Millennium from Rhode Island Fast Ferry for one year for $2.5 million. Millennium allowed full service to continue while Marin and Sonoma underwent major work and the other ferries received regular maintenance. The Millennium remained in service until 2020 before returning to Rhode Island.
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When MS Golden Gate retired in 2004, it had made 42,108 round trips between Sausalito and San Francisco, carried 21 million passengers, and traveled nearly 1.3 million nautical miles (2,400,000 km; 1,500,000 mi).