The original Early Bird Express network introduced in February 2019 had fifteen routes, but some were eliminated later that year due to low ridership.

Smaller systems include Emery Go-Round in Emeryville, Commute.org on the Peninsula, San Leandro LINKS, Dumbarton Express, and Union City Transit.

[20] Marvin E. Lewis, a San Francisco trial attorney and member of the city's board of supervisors spearheaded a grassroots movement to advance the idea of an alternative bay crossing and the possibility of regional transit network.

Although invited to participate, Santa Clara County supervisors elected not to join BART due to their dissatisfaction that the peninsula line only stopped at Palo Alto initially, and that it interfered with suburban development in San Jose, preferring instead to concentrate on constructing freeways and expressways.

Another important factor in Marin's withdrawal was an engineering controversy over the feasibility of running trains on the lower deck of the Golden Gate Bridge, an extension forecast as late as three decades after the rest of the BART system.

[33] Ridership remained well below projected levels throughout the 1970s, and direct service from Daly City to Richmond and Fremont was not phased in until several years after the system opened.

As early as 1969, before revenue service began, several BART engineers identified safety problems with the Automatic Train Control (ATC) system.

[34] Less than a month after the system's opening, on October 2, 1972, an ATC failure caused a train to run off the end of the elevated track at the terminal Fremont station and crash to the ground, injuring four people.

A 2010 study[62] concluded that along with some Bay Area freeways, some of BART's overhead structures could collapse in a major earthquake, which has a significant probability of occurring within three decades.

[6][78] The Oakland Airport Connector uses a completely separate and independently operated fleet of cable car-based automated guideway transit vehicles.

[84][85] This was originally introduced to allow people to tour the then-futuristic system; it was kept to discourage undesired behaviors such as tech bus riders using BART parking lots.

[92] It was the third system in the US to use encoded-value magnetic stripe tickets, following the Illinois Central Gulf commuter line (now the Metra Electric District) in 1964 and the PATCO Speedline in 1968.

[95] However, due to supply chain shortages resulting in a lack of plastic Clipper cards, BART started issuing tickets again at the SFO station in October 2022.

[101] A major exception occurred in 1989 in the aftermath of the Loma Prieta earthquake, which severely damaged the San Francisco–Oakland Bay Bridge, causing its closure for a month.

[105] The Washington Post and LA Streetsblog attributed the national decline in ridership to changes in commute patterns, the fall in gasoline prices since 2014, and competition from the private sector in the form of ride-hailing services such as Uber and Lyft.

[111] BART's one-day ridership record was set on Halloween of 2012 with 568,061 passengers attending the San Francisco Giants' victory parade for their World Series championship.

[116] BART set a Saturday record of 419,162 riders on February 6, 2016, coinciding with Super Bowl 50 events and a Golden State Warriors game.

[117][118] That easily surpassed the previous Saturday record of 319,484 riders, which occurred in October 2012, coinciding with several sporting events and Fleet Week.

[121] If ridership does not recover and additional revenue is not obtained, in the worst case the agency projected it would only be able to sustain trains on three lines running once an hour from 5am to 9pm weekdays, and would have to close nine stations.

The section of the Antioch-SFO/Millbrae line east of the Pittsburg/Bay Point station, known as EBART, runs on conventional unelectrified 4 ft 8+1⁄2 in (1,435 mm) standard gauge rail.

The additional double-tracked four-mile-long (6.4 km) upper deck of the Market Street subway and its four underground stations were built by BART for Muni Metro.

[138] BART has begun to correct this issue at stations either by expanding the paid area on the concourse level or by installing a single accessible faregate in front of the elevator doors.

[141] In 2004, BART became the first transit system in the United States to offer cellular telephone communication to passengers of all major wireless carriers on its trains underground.

[146] Service was made available for customers of Verizon Wireless, Sprint/Nextel, AT&T Mobility, and T-Mobile in and between the four San Francisco Market Street stations from Civic Center to Embarcadero.

[152] The ensuing controversy drew widespread coverage[153] that raised legal questions about free speech rights of protesters and the federal telecommunications laws that relate to passengers.

[161] (BART management claimed that in 2013, union train operators and station agents averaged about $71,000 in base salary and $11,000 in overtime, and pay a $92 monthly fee from that for health insurance.

Oakland civil rights attorney John Burris filed a US$25 million wrongful death claim against the district on behalf of Grant's daughter and girlfriend.

[186][187] On August 29, 2011, a coalition of nine public interest groups led by Public Knowledge filed an Emergency Petition asking the U.S. Federal Communications Commission (FCC) to declare "that the actions taken by the Bay Area Rapid Transit District ("BART") on August 11, 2011, violated the Communications Act of 1934, as amended, when it deliberately interfered with access to Commercial Mobile Radio Service ("CMRS") by the public" and "that local law enforcement has no authority to suspend or deny CMRS, or to order CMRS providers to suspend or deny service, absent a properly obtained order from the Commission, a state commission of appropriate jurisdiction, or a court of law with appropriate jurisdiction".

[195] On the afternoon of October 19, 2013, a BART employee and a contractor, who were inspecting tracks, were struck and killed near Walnut Creek by a train being moved for routine maintenance.

According to an internal memo, the agency decided to not issue a press release about one of the cases (where a woman had her phone stolen by one of a group of teenagers) in order to avoid having BART look "crime ridden" and because it would "unfairly affect and characterize riders of color, leading to sweeping generalizations in media reports.