The first regular crossing of the Carquinez Strait began in the mid-1800s as a ferry operated between the cities of Benicia and Martinez, six miles upstream from the bridge site.

The preferred option, given the engineering limitations of the day, was to skirt around the Delta by going south from Sacramento through Stockton, then proceeding west across the San Joaquin River and over the Altamont Pass, and finally reaching Oakland from the south; a route that would later become U.S. Route 50 and ultimately Interstates 5, 205, and 580.

This circuitous route, several miles longer, and traversing a rather formidable mountain pass, was preferable to crossing the Carquinez Strait, a deep channel with strong currents and frequent high winds.

For decades, building a bridge across the Carquinez Strait was considered prohibitively expensive and technologically risky.

The Carquinez Bridge provided a welcome alternative route from the Central Valley to the Bay Area, one that no longer required loading one's vehicle onto and off of a ferry.

With the bridge completed, the Lincoln Highway was realigned to cross the Sacramento River, then proceed southwest through Davis and Vallejo, across the Carquinez Bridge, and along the shores of the San Pablo and San Francisco bays to Richmond and Oakland; becoming U.S. Route 40, and ultimately Interstate 80.

After the Loma Prieta earthquake engineers determined that the aging 1927 span was seismically unstable, and that a retrofit was impossible.

The bell will eventually be displayed in a new museum to be built at the Oakland end of the San Francisco–Oakland Bay Bridge.

Originally, the plan was to dedicate the bridge on November 15, but complications involving then just-recalled Governor Gray Davis and the transfer of power to Arnold Schwarzenegger resulted in the date being moved.

It features a pedestrian and bicycle path, part of a bike trail which it is hoped will eventually circle the entire Bay Area.

Additional field investigations during construction revealed significant variations in rock conditions at the North Tower, resulting in the redesign of the length of the piles.

[11] A $1 seismic retrofit surcharge was added in 1998 by the state legislature, increasing the toll to $2 (equivalent to $3.74 in 2023), originally for eight years, but since then extended to December 2037 (AB1171, October 2001).

[12] On March 2, 2004, voters approved Regional Measure 2 to fund various transportation improvement projects, raising the toll by another dollar to $3 (equivalent to $4.84 in 2023).

Caltrans administers the "second dollar" seismic surcharge, and receives some of the MTC-administered funds to perform other maintenance work on the bridges.

The Bay Area Toll Authority is made up of appointed officials put in place by various city and county governments, and is not subject to direct voter oversight.