Double Crossing San Francisco Bay

Link21 Program Calls New Rail Tunnel Linking San Francisco and Oakland Critical to Improving Region’s Passenger Service and Reducing Car Dependency

Key System train crossing San Francisco Bay. From 1939 until it closed down in 1958 the Key System ran to the Transbay Terminal.

Before Amtrak you could ride Union Pacific’s City of San Francisco (run collaboratively with Southern Pacific and Milwaukee Road) or Santa Fe's San Francisco Chief. But they couldn’t take you into the city they were named for. Oakland and Richmond, CA, respectively, were their last stops. At the end of the line you transferred to a bus that crossed the San Francisco – Oakland Bay Bridge and dropped you off at Transbay Terminal.

The same applied to the California Zephyr when it was operated jointly by the Burlington, Rio Grande, and Western Pacific Railroads. Fifty five years later, Amtrak passengers still must transfer to another mode reach the City on the Bay.

Rail service across the Bay has an interesting history. The San Francisco – Oakland Bay Bridge was built with railroad tracks on the lower level. From 1939 to 1958 the Key System used them to reach Transbay Terminal. The Sacramento Northern and Southern Pacific’s Interurban Electric Railway subsidiary briefly ran over the bridge, as well.

Around the time the Key System closed officials started to plan a new rapid transit line that would run under San Francisco Bay instead of above it. The BART (Bay Area Rapid Transit) system opened its first route in 1972. After a 24-years hiatus trains ran between San Francisco and Oakland. Today BART operates five routes in the Bay Area that extend from the two cities’ downtowns to Millbrae, Richmond, Antioch, Dublin/Pleasanton, and North San Jose.

BART has been enormously successful. In 2024 it had 50,656,380 riders making it the seventh busiest U.S. rapid transit system. Currently it is building a six-mile extension from North San Jose to downtown San Jose and Santa Clara that could serve an additional 55,000 passengers daily.

Although it connects with Amtrak in Richmond, BART does not serve its Jack London Square (Oakland) and Emeryville stations. In addition, its broad gauge track (5’6”) is incompatible with other rail lines in the region.

Transit planners want to address unmet travel needs for a much larger area. They view Northern California as a megaregion composed of 164 cities, 21 counties, and four regions. These are: the greater San Francisco Bay Area; the Monterey Bay area; the Sacramento area, and the Northern San Joaquin Valley. It is home to 12.7 million Californians, 31.7 percent of the state’s population, with another two million expected by 2050.

Northern California has a fragmented passenger rail system with different routes, types of services, and operators. Riders must contend with infrequent service, long travel times, and time-consuming transfers that require multiple tickets. When it comes to crossing San Francisco Bay BART is the only train in town. During peak hours it often runs standing room only.

Consequently a relatively small share of trips in the region are made by train. BART can get someone living Concord to a job in downtown San Francisco or Oakland, but what if they want to hit the beach at Santa Cruz or visit Palo Alto? Unless they are willing to endure multiple transfers and lengthy waits the region’s congested highways are their only choice.

Link21 is a program of improvements to better connect BART with regional rail lines. As envisioned by the California State Rail Plan, the projects to be Included are intended to make train travel a better option for people who live and work throughout the Northern California Megaregion.

The most important item on its list is a second rail crossing of San Francisco Bay. Completion of this tunnel is expected to improve service and reliability and make it easier to take a train to more destinations in the Megaregion.

This could bring relief to the existing bridge and rail line that comprise the San Francisco – Oakland transportation corridor, which ranks among the most congested in the country. With additional capacity the region’s rail network could add new routes that would enable one-seat rides between the greater Sacramento area and Silicon Valley, for example.

In a report released in 2021, the Bay Area Council Economic Council noted the migration from the Bay Area to Sacramento driven by the search for affordable housing. As people moved further from where they work their commute times increased. Of the 187,000 people who were commuting into in the Bay Area in 2018 95 percent were driving.

Sixty nine percent of the Northern California megaregion’s 5.8 million jobs are located in the Bay Area. But the nine counties that comprise the region – San Francisco, Marin, Sonoma, Napa, Solano, Contra Costa, Alameda, Santa Clara, and San Mateo – are home to just 61 percent of the population.

The other three regions - Monterey Bay area, Sacramento area, and Northern San Joaquin Valley – all have smaller shares of the megaregion’s jobs but larger shares of its population.

As people moved further from their jobs their commutes lengthened. Between 2010 and 2018 the percentage of Bay Area workers with commutes longer than 50 minutes rose from 11 percent to 19 percent. Nearly one-fourth of people working in San Francisco and San Mateo counties had commutes longer than 50 minutes.

At the same time 29 percent of people who worked in the Bay Area rode transit to get to the office. However, only 12 percent of those who lived beyond the Bay Area took transit. The Council attributes this to lack of direct routes between the outer counties and the San Francisco Peninsula.

A new Transbay rail crossing would unlock the potential of other rail improvements planned for the megaregion, the Council observed. With increased access to San Francisco and the Peninsula the upgrades “will form a megaregional rail network that can serve customer needs across the Bay Area, Sacramento, and the northern San Joaquin Valley and provide a much greater percentage of total trips in the Northern California Megaregion.”

Link21’s market analysis shows more people would travel by train if they were more convenient. However, the new tunnel is needed to meet that demand since 45 percent of trips that could potentially be made by train would involve crossing San Francisco Bay. This includes trips that originate in San Francisco or Oakland in addition to people traveling into the Bay Area from the Northern California Megaregion’s three other regions.

The new tunnel would strengthen the business case for other improvements throughout the Megaregion. A list of potential projects, which includes line extensions, new stations, service improvements, and infrastructure upgrades, can be found on the Link21 website. One proposal – a new bridge on the Capital Corridor to replace the Benicia – Martinez Rail Bridge across Carquinez Straight – has a $10 billion price tag.

Recently the Link21 directors chose standard gauge track for the new tunnel instead of the broad gauge used by BART. This will result in an open network that can run over existing rail lines and is accessible to regional and intercity trains whereas BART operates as a closed system.

With Link21 still in early planning stages and deciding which projects to advance to environmental review the first shovel isn’t likely to be turned for several years. But the program’s potential scope and impact on rail service in the Bay Area, specifically, and the entire Northern California Megaregion makes it worth following. And who knows? Maybe someday the California Zephyr will run to San Francisco instead terminating in Emeryville.