AC Transit provides bus service around the inner East Bay, including parts of both Alameda and Contra Costa counties. From north to south: Richmond, El Cerrito, Albany, Berkeley, Emeryville, Oakland, Alameda, San Leandro, Castro Valley, Hayward, Union City, Newark, and Fremont. Around the core Oakland/Berkeley area, service is good: most attractions of interest are served and buses run pretty frequently, usually at least twice an hour and every 10–15 minutes for core routes. As you move away from this core area, service gets more sparse. You can pay by cash or get a slight discount with a Clipper card.

A few lines extend to San Francisco, Palo Alto, Menlo Park, and Milpitas (near San Jose).

• Line U East Bay Express. Commuter shuttle service, with luxury coach seating, going from 37.5574-121.97581 Fremont BART to Stanford University in the morning and the opposite direction in the evening. $4.20; free with Stanford ID.

An Amtrak-run commuter train running from the Central Valley towns of Stockton, Tracy, Livermore and Pleasanton to San Jose. It runs only a few times a day - as of 2017, there are 4 southbound trips (to San Jose) each morning, and 4 northbound trips in the afternoon/evening, so be sure to check the schedule ahead of time.

The train shares the Santa Clara station with Caltrain. It also stops at the Great America station at Lafayette and Tasman, near the Santa Clara Convention Center, Levi's Stadium, and California's Great America.

See the Santa Clara and San Jose articles for information on free shuttles which are timed to connect to ACE trains at the Great America, Santa Clara, and San Jose stations.

BART is a metro-regional rail hybrid which connects San Francisco, the East Bay cities, northern San Mateo county, and northeastern San Jose, with five lines as well as spur services to Oakland Airport and the city of Antioch. Four of the five lines serve San Francisco, while a fifth, the Orange line, connects the northern San Jose neighborhood of Berryessa to the city of Richmond through Fremont, Oakland, and Berkeley. Two of the San Francisco lines, the Blue and Green lines, start in Daly City, with both lines running concurrently through the Mission, Downtown San Francisco, Oakland, and the southern parts of the East Bay. The Blue line separates from the Green Line at Bay Fair station to serve Castro Valley and eventually terminating at Dublin Pleasanton, while the Green line runs concurrently with the Orange line to Berryessa. The other two San Francisco lines, the Yellow and Red lines, each begin further south at San Francisco International Airport (SFO); the Red line temporarily turns further south to Millbrae and a connection to Caltrain before rejoining the Yellow line at San Bruno station, to which the Yellow line runs directly to from SFO. The two lines serve South San Francisco and Colma before running concurrently with the Blue and Green lines between Daly City and West Oakland; the Yellow and Red lines serve downtown Oakland's 12th and 19th streets as opposed to the Blue and Green serving Lake Merritt and the neighborhood of Fruitvale. The two lines diverge after MacArthur station; the Red line travels concurrently with the Orange line to Richmond via Berkeley, while the Yellow line continues on its own to Pittsburg and Bay Point through Concord and Walnut Creek. Through a spur line known as eBART, travelers on the Yellow line can travel as far as Antioch.

When used solely within San Francisco, BART is only useful for traveling to the Mission without resorting to buses. The SFMTA's Muni services cover much more of the city, though residents of San Francisco and visitors staying for a month or longer can add a 30-day long Muni pass to a Clipper card which gives unlimited rides on both all Muni services and BART between Balboa Park and Embarcadero stations. For visitors solely to San Francisco proper, outside of the Mission and excluding taxis or car transportation, BART is the quickest way to the airport and back. During rush hour, BART can be faster than taxis and ridesharing.

In terms of safety, visitors should exercise normal precautions for visiting any subway system. Powell Street station is a regular destination for both the homeless and protesters; the station is also the closest to Union Square and the cable cars. In general, though, BART is not a dangerous system, and unlike other subway systems, patrons are free to move between the gangways of train cars. Passengers who require wheelchairs or elevators will find that BART is very friendly; the agency encourages customers to use its mobile app to find out if and where any elevators are out of service. Accessible fare gates are also present at every station, marked with a yellow-orange instead of the normal red-colored wedges.

Fares on BART are calculated by distance, ranging from $2.15 for all stops within San Francisco to $17.60 for a trip between SFO and Oakland Airports. BART is the quickest method of transit between SFO and downtown San Francisco (which costs $10.00), and during rush hour, the trains can be faster than traffic. To pay for BART, tag a Clipper Card at the fare gate upon entering and exiting the BART system; audible announcements as well as overhead signs will direct you to platform level and which train is coming next, as well as estimated wait times. Trains are named by their terminating station; as an example, boarding a Berryessa Train at a Downtown San Francisco station will direct you to the southern part of the East Bay. Should you end up needing to add more money to your Clipper card before leaving, there are highly visible "add fare" machines at each station both within and outside of the paid area. Passengers who enter and exit through the same station within 3 hours in a single trip will be charged an "excursion fare" of around $6.70; while the BART board has voted to discontinue excursion fares, these will not fully be removed until around 2024.

BART's normal service is from 4:30 AM to 9 PM local time; around 9 PM, trains will switch to a three-line service. This means that the Red and Green lines will stop service, meaning that there will be no direct services from San Francisco to Berryessa and Richmond. To compensate, BART designates certain stations as recommended for transfers. In particular, northbound trains on the Yellow and Orange lines to Antioch and Richmond are scheduled to arrive at the same time, so that passengers can walk from one train to the other on the same platform. Southbound trains to SFO and Berryessa on the Yellow and Orange are programmed the exact same way, though at MacArthur station instead of 19th Street Oakland. Transfers between the Blue and Orange line, while theoretically possible at any station between Bay Fair and Lake Merritt, are preferred by BART at Bay Fair station. Around midnight, the system begins to shut down for the night, with en route trains finishing their last journey around 1:10 AM at the latest. BART frequency is pretty good: trains run at least every twenty minutes, assuming no delays or disruptions, and multiple lines share the same tracks so for popular journeys the wait is usually less. Overnight transbay service can be achieved using AC Transit buses, and late night service from San Francisco to SFO is handled by SamTrans buses.

The same Clipper card you used to pay your BART fare can also be used to transfer to other transit agencies. Multiple Bay Area transit agencies provide credits when transferring to or from BART using Clipper. The current information can be found on Clipper's BART page.

Most BART stations have restrooms.

Bicycles can be brought on BART trains and are a reasonably common sight. Each car has a designated area for bicycles, and you're allowed to bring one on as long as the train isn't crowded (avoid rush hour) and you don't bring it into the train's first car. You can get it to the platform by elevator or escalator. See the official website for detailed information about bikes on BART.

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, once an hour late evenings, and once every hour on 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. Most trains don't stop at every station, so look at the schedules to check.

If transferring between Caltrain and BART, the cheapest option is to transfer in Millbrae (the southernmost BART station on the Peninsula). Get off in Millbrae and follow the signs to make your connection. Transferring between northbound Caltrain and BART can be done as a cross-platform transfer, although you may need to hunt for the open gate; between southbound Caltrain and BART you need to ascend to the second level (which is quite high up) and then descend to the desired platform, so do allow more time. Use Clipper to tag in/out of BART and Caltrain separately, as their fare structures are separate.

Golden Gate Transit is the backbone of transportation between San Francisco and the North Bay, with buses up and down SF, Marin, and Sonoma counties, a couple of lines to the East Bay, and ferries between the city and Marin (see #Ferries). It's easy to make connections to the other transit systems that serve these areas.

If using a Clipper card, make sure to tap on and off Golden Gate Transit buses so you aren't overcharged.

MAX runs service primarily geared for commuters who live in Modesto and work in the Bay Area. Limited reverse-commute service is available on some lines; call for details. Reservations are recommended, as preference is given to monthly-pass holders. Individual fares are cash only; exact change is required.

• Modesto BART Express, ☏ +1 209 521-1274. M–F, except holidays. Two AM and two PM buses between Modesto and the Dublin/Pleasanton BART station. No bike racks (unlike other MAX buses). $14 one-way; $16 same-day round trip. (updated Feb 2016)
• Modesto ACE Express, ☏ +1 209 521-1274. M–F, except holidays. Service between Modesto and the Manteca/Lathrop ACE station. $3 one-way. (updated Feb 2016)

In its heyday the system of ferries all around the Bay Area was extensive. Nowadays bridges and BART mean that ferries have been reduced to a handful of key lines, but they are still an important form of transportation for some commuters and local daytrippers, a backup option for when bridges are incapacitated by earthquakes and other emergencies, and lovely way to enjoy the great weather and views of the bay.

Golden Gate Ferry goes from San Francisco to Larkspur, Sausalito, and Tiburon in Marin County. The ferry to Sausalito in particular is a popular way to reach the little waterfront town for fine dining and views of the city. The ferry to Larkspur allows connections to other parts of Marin, and from Tiburon it's possible to take another ferry to Angel Island for hiking.

The San Francisco Bay Ferry connects San Francisco to several locations in the East Bay and the North Bay, including Alameda, Oakland, Richmond, and Vallejo.

Other ferry lines go to key attractions like Alcatraz and Angel Island.

Not public transit in the strictest sense of the term, but the various airporters (scheduled airport shuttles) offer airport connections that are more convenient than the regular buses and more affordable than a taxi, especially for the North Bay. In general, plan to pay in cash or by online reservation. Clipper cards are not accepted.

The Bay Area has three main airports: San Francisco International Airport (SFO ^IATA), Oakland International Airport (OAK ^IATA), and San Jose International Airport (SJC ^IATA). There's also a small Sonoma County Airport (STS ^IATA) near Santa Rosa.

• Groome Transportation. Every two hours, early morning to late evening. Goes from SFO and Sonoma County Airport to several destinations in Sonoma County (Petaluma, Rohnert Park, Santa Rosa), as well as from OAK to Marin and Sonoma Counties (San Rafael, Petaluma, Rohnert Park, Santa Rosa, and Sonoma County Airport). $48 to Sonoma County, $37 to Marin County; $2 discount for seniors, military, and students under 21 with ID; one child 12 or under free per adult. 
• Evans Airport Shuttle. Seven days a week, about every two hours morning to evening. OAK and SFO to Vallejo and Napa. $40 per person; children 12 and under to Napa is only $30. 
• Marin Airporter. Every 30 minutes, 5AM to midnight, but transport to the airport may be less frequent depending on where you get on. SFO to Marin County. Stops in Sausalito, Mill Valley (Manzanita and Seminary Drive), Larkspur Landing, San Rafael (Anderson Drive and the Transit Center), and Novato). $23, paid when you get off the bus. (updated Jun 2019)
• Monterey Airbus. SFO and SJC to Prunedale, Marina, and Monterey—all in Monterey County, south of the Bay Area. 
• Santa Cruz Airport Flyer. SFO and SJC to Scotts Valley, Santa Cruz, and Aptos—all in Santa Cruz County, south of the Bay Area. 

An outgrowth of the Humphrey Go-Bart shuttle launched in the 1970s, Bear Transit offers daytime weekday (M-F) service around the UC Berkeley campus and beyond, including BART stations, the 37.8753-122.23862 UC Botanical Gardens, 37.8802-122.24623 Lawrence Hall of Science, downtown Berkeley, and points in El Cerrito and Richmond. General public: $1–$1.50. Info at 511.org web site but not on their phone line.

• Emery Go-Round, ☏ +1-510-451-3862, [email protected]. Shuttle service for residents, workers, and visitors to the city of Emeryville. Two standard routes and three commute routes run to and from Oakland's MacArthur BART station. Free. (updated Jul 2020)

Easily the best transit bargain in the Bay Area—free to everyone—Marguerite buses traverse the Stanford University campus, with most routes stopping at the 37.4332-122.17684 Medical Center, 37.4421-122.16955 Shopping Center, and 37.4438-122.1656 Palo Alto Transit Center (for connections to VTA, SamTrans, and Caltrain). Some lines extend farther beyond the campus, to: 37.5574-121.97587 Fremont BART (lines AE-F, EB); 37.5902-122.01738 Union City BART Station (line EB); 37.4542-122.1829 Menlo Park Caltrain station and 37.4808-122.176510 Bohannon Drive (line BOH); 37.4201-122.202511 Linear Accelerator (lines S, SLAC); 37.405-122.140412 VA Palo Alto Health Care facility (lines R, RP, VA); 37.4505-122.114413 Palo Alto Tech Center, 0.3 miles from 37.4547-122.115214 Palo Alto Airport (line TECH); 37.3947-122.146415 Research Park (lines 1050A, RP). Unfortunately, Marguerite information is not on the 511 system.

Marin Transit provides bus service in Marin County. In addition to connecting the Marin County cities, it offers a seasonal shuttle to Muir Woods (buses 66 and 66F), and the West Marin stagecoach goes to Stinson Beach (bus 61) and Point Reyes (bus 68). The system's biggest hub is the San Rafael Transit Center in San Rafael, with smaller hubs in Novato, San Anselmo, and Marin City (near Sausalito). Connections to Golden Gate Transit buses to San Francisco, Richmond, and Sonoma County are available.

Marin Transit's service is sometimes late and not always convenient, but if you're visiting Marin without a car, it gets the job done.

See also: San Francisco#By public transit

• San Francisco Municipal Transportation Agency (Muni), ☏ +1-415-701-2311. Offers light rail and bus service throughout San Francisco, including San Francisco's famous cable cars. (updated Jul 2020)
  • Rail and buses. Single-ride fares valid for unlimited travel within 2 hours. Special 1/3/7-day Visitor Passports are available for unlimited travel on MUNI and cable car routes. Adults: $3.00 single ride, 50-cent discount for using a Clipper card or their mobile app. Youth (5-18), seniors (65+), and disabled riders: $1.50 single ride, 25-cent discount for Clipper or mobile app.. (updated Jul 2020)
  • Cable cars. Special 1/3/7-day Visitor Passports are available. $8.00 single-ride fare for all riders; Half-price for seniors/disabled/medicare between 9PM-7AM. (updated Jul 2020)

• Santa Clara Valley Transit Authority (VTA), ☏ +1-408-321-2300, [email protected]. Offers light rail and bus service throughout Santa Clara County. Single-ride fares valid for unlimited transfers within 2 hours when using Clipper or EZPass. If using a Clipper card, you will automatically stop being charged when you reach the daily rate through VTA's "Day Pass Accumulator" program. Adults: $2.50 single ride, $5.00 8-hour light rail pass, $7.50 day pass. Youth (5-18) get 50% off adult fares. Seniors (65+)/disabled get 60% off adult fares. (updated Jul 2020)
  • Light rail. The Blue, Green, and Orange lines connect Mountain View, Sunnyvale, Santa Clara, Milpitas, San Jose, and Campbell. These lines are faster than regular buses, but are still a bit slow through downtown San Jose. Buy your ticket on the platform before boarding train. You can freely transfer between light-rail lines but must complete your trip within 2 hours. Bikes are allowed on board and are hung vertically from hooks at the end of cars. If your bike is heavy or loaded with panniers, this can be difficult. (updated Jul 2020)
  • Local, Frequent, and Rapid buses. Bus routes are "frequent" if they run every 15 minutes or better between 6:30AM-6:30PM. "Rapid" buses provide faster service than the corresponding regular buses because they skip many smaller stops; there are three Rapid routes, 522, 523, and 568 which correspond to regular routes 22, 23, and 68; as well as the 500. Adults: $2.50 single ride, $7.50 day pass. Youth (5-18) get 50% off adult fares. Seniors (65+)/disabled get 60% off adult fares.. (updated Jul 2020)
  • Express buses. These routes use freeways to travel longer routes. Generally geared towards commuters rather than tourists. Note that these have higher fares! Adults: $5.00 single ride, $15.00 day pass. There is no surcharge for youth (5-18), seniors (65+), and disabled riders, who pay the same fares as they would for local buses.. (updated Jul 2020)
  • Shuttles. Shuttle routes provide connections for riders of ACE to various Silicon Valley companies. Free. (updated Jul 2020)

Sonoma-Marin Area Rail Transit (SMART) is a rail line opened in 2017 that connects Marin County and Sonoma County, with stops at Sonoma County Airport, Santa Rosa, Rohnert Park, Petaluma, Novato, San Rafael, and Larkspur. An extension is planned to Cloverdale. Fares depend on a zone system and must be paid by Clipper card or an "eTickets" app. During peak commuter hours, service is roughly every 30 minutes, but on weekends it's only once every hour or two.

The Larkspur station allows connections to Golden Gate Ferry.

The segment between Petaluma and Novato is quite scenic, with views of the North Bay hills and marshland.

Serves Pinole, Hercules, and the surrounding area, between Richmond and Martinez. Buses from El Cerrito Del Norte BART to and from Pinole and Hercules run often enough to be useful, in the unlikely event that you need to get to those towns.

Basic fare is $2. Transfers between Wheels buses or to ACE are generally free. A transfer from BART costs $1.

You may not need a card to use public transit in the Bay Area, since you can always deposit money into a fare box or ticket machine; however, on BART or SMART, this will require you to purchase a Clipper card as part of the fare purchase. The card costs $3, plus the money you pre-pay for rides, so it may not make sense if you plan to take only a few rides on public transit. On the other hand, some agencies (e.g. BART, Muni, Caltrain) charge less for tickets purchased with Clipper. Savings can be even greater when you take several rides on the same day. For instance, the Santa Clara Valley Transportation Agency (VTA) no longer issues transfers or day passes, but the maximum daily amount that is charged to the card of an adult (age 19–64) for non-Express rides on the system is $7.50, the cost of 3 individual adult rides. Also, fare discounts for some inter-system transfers (e.g., between BART and a local bus) are given only to those using a Clipper card. An additional factor to weigh is the convenience of not having to deposit exact change into fare boxes, versus the inconvenience of buying and recharging the card.

Clipper cards for adults can be purchased for $3 at most Bay Area Walgreens and Whole Food stores, other retail locations, and at BART or SMART stations. Youths (age 5 to 17 or 18, depending on the transit agency), seniors (65 or older), and the disabled are eligible for special cards that are good for discounted rides. You can get these from a Regional Transit Connection center (typically, the offices of the local transit agency) or by mail (allow 10 days for delivery). For details, go to the Clipper card website or call one of the customer service numbers listed in section For more information, below. Allow 10 days for delivery.

Alternatively, instead of a plastic card, you can get a digital Clipper card on a smartphone using Apple Pay or Google Pay.

Once you have the card, you can add cash value to it at any of the retail locations, online, or at BART (cash only), VTA light-rail, or SF Muni ticket machines. Some Caltrain stations also have Clipper Add-Value machines. The first time you add value online, there will be a delay of a few days before it appears on your card.

Clipper card readers are located on buses and at train stops. Hold the card next to the reader. It is not usually necessary to remove the card from your wallet. The reader display will indicate whether the payment was successful, and how much money is left on the card.

For some systems, like BART, Caltrain, and many buses, the fare varies by distance traveled. So you need to tap the card twice - upon beginning and ending your ride - so that you are charged the correct fare. (If you forget to "tap out" at the end of your Caltrain ride, you may be charged a higher fare.) On other buses, you only need to tap when you get on. Ask the driver if you're not sure, or look at what other passengers are doing.

Questions specifically about Clipper cards are addressed at the Clipper web site (www.clippercard.com), via e-mail ([email protected]), or on their customer-service phone lines (voice: +1-877-878-8883; fax: +1 925 686-8221; TDD/TTY: +1-800-735-2929). For more information about all of the Bay Area transit systems, go to 511.org, or call 511 from a phone from within the Bay Area.