By train
Bay Area Rapid Transit BART (http://www.bart.gov) is an extensive regional metro system that connects San Francisco to the East Bay and Contra Costa County, as well as parts of the Peninsula, the eastern half of Silicon Valley, and the San Francisco and Oakland airports. BART is also useful for getting around within SF and Oakland. Ticket prices vary by distance traveled, but usually run about $2-5 one way and tickets can be purchased from vending machines at any station. You will need to insert your ticket into barriers when entering and exiting the system. Tickets hold a balance, deducting the appropriate price for each trip, so someone who plans to use the system several times can buy a $10 or $20 ticket and not worry about fares until the card is used up. Note that the BART vending machines accept any credit card only twice within any 24 hour period. Trains run about every 10-20 minutes starting around 6AM and closing just after midnight.
Caltrain is a commuter train system running along the Peninsula between San Francisco, San Jose and Gilroy. Ticket prices vary by the distance between stations, but usually run around $3-$6 one way. Trains run about once every half hour, on average, once an hour late evenings and weekends, with several more trains running during commute hours. This train service is not particularly fast; however, in a move to improve speed, many trains during commute hours run express or semi-express service, so they do not stop at all stations. Tickets must be purchased before boarding the train from ticket vending machines at any of the stations or from ticket clerks at staffed stations. Tickets are checked on the trains and anyone found without a ticket is liable to a substantial fine. Cyclists should use the designated car at the northern end of the train, and be aware that bike space is often limited during commute hours.
A full list of Bay Area public transportation agencies, as well as a refreshingly useful trip planner, can be found at the Metropolitan Transportation Commissions's web site 511.org .
By ship
Passenger ferries link many of the cities in the Bay Area particularly the North Bay, and can be a very scenic way to get around, with splendid views of the San Francisco skyline, Alcatraz, and much of the lush hillside scenery. In San Francisco, the ferries dock at one or both of the city's two piers at Fisherman's Wharf and the Ferry Building, the later of which is a very short walk from extensive BART and Muni services. In Oakland, the ferry terminal is at the foot of Clay Street in Jack London Square. There are five operators of ferry services in the Bay Area:
Golden Gate Ferries
+1 415 455-2000 (http://www.goldengateferry.org). Runs regular service between San Francisco and Larkspur and Sausalito.Blue and Gold Fleet
+1 415 705-8200 (http://www.blueandgoldfle...). Runs ferries between San Francisco and Sausalito, Alameda/Oakland, Tiburon, Vallejo, and Angel Island, with additional service to Angel Island from Alameda/Oakland and Vallejo.BayLink Ferry
+1 877 643-3779 (http://www.baylinkferry.com). Offers service between San Francisco and Vallejo.Alameda Oakland Ferry
+1 510 522-3300 (http://www.eastbayferry.c...). Runs ferries between Alameda/Oakland and San Francisco and Angel Island.Harbor Bay Ferry
+1 510 769-5500 (http://www.alamedaharborb...). Runs service between Alameda and San Francisco.