Workers representing two of BART's largest unions went on strike after talks with management broke down on Sunday. No new talks have been scheduled.
The striking unions and management reported being far apart on key sticking points that included salary, pensions, health care and safety.
"Our members aren't interested in disrupting the Bay Area, but management has put us in a position where we have no choice," said Antonette Bryant, president of Amalgamated Transit Union Local 1555.
The unions, which represent nearly 2,400 train operators, station agents, mechanics, maintenance workers and professional staff, want a 5 percent raise each year over the next three years.
BART said train operators and station agents in the unions average about $71,000 in base salary and $11,000 in overtime annually. The workers also pay a flat $92 monthly fee for health insurance.
BART spokesman Rick Rice said the agency had upped its original offer of a 4 percent pay increase over the next four years to 8 percent. The proposed salary increase is on top of a 1 percent raise employees were scheduled to receive Monday, Rice added.
The transit agency also said it offered to reduce the contribution employees would have to make to pensions, and lower the cost for health care premiums.
BART, with 44 stations in four counties and 104 miles of lines, handles more than 40 percent of commuters coming from the East Bay to San Francisco, said John Goodwin, a spokesman for the Metropolitan Transportation Commission.
Transit authorities have made accommodations to help, including longer carpool lane hours, additional ferries, and extra buses. BART doubled the number of buses serving West Oakland to 36 on Tuesday.
Stuart Cohen, executive director of TransForm, a nonprofit organization focused on public transportation and walkable communities in the Bay Area, suggested employers allow workers to telecommute.
"Truth is, on a nice summer day, it's good to telecommute," he said.
"Hopefully this won't go too long. It if continues into a non-holiday week next week, we're going to find a lot of people settling into new patterns, finding carpools," he said. "I think this experimentation could settle in a bit, and if it lasts long enough, I'd expect when BART service comes back ridership will be down."
Mihir Zaveri reported from Berkeley, Calif. Follow Martha Mendoza at https://twitter.com/mendozamartha .