Members of the BART chapter of Local 1021 of the Service Employees International Union, which represents about 1,400 mechanics, custodians, safety inspectors and clerical employees, shot down the contract with 98.5 percent of voters rejecting it.
"Monday we start all over and we go to the contract negotiation table," Local 1021 spokesman Carlos Rivera said.
Members of Amalgamated Transit Union Local 1555, which represents about 900 train operators, station agents and power workers, rejected the contract on Tuesday.
ATU Local 1555 President Jesse Hunt said about three-quarters of his members participated in the vote and that all of them cast "no" votes.
There are three other BART unions, but they haven't scheduled votes so far.
Jean Hamilton, the president of BART's third-largest union, Local 3993 of the American Federation of State, County and Municipal Employees, which represents about 200 middle managers, said she hasn't scheduled a vote for her members because she needs to get more information from management.
Members of ATU Local 1555, SEIU Local 1021 and AFSCME Local 3993 all voted overwhelmingly last month to approve a strike if a settlement isn't reached on a new contract. However, union leaders haven't yet called for a strike and say they want to continue negotiations with management.
There are two small unions that represent BART police officers and managers but they're barred from going on strike.
BART spokesman Linton Johnson has said the most likely next step in the negotiating process, which began April 1, is that contract talks will resume Monday afternoon.
Johnson said BART's management believes its contract offer is responsible because it saves $100 million in labor costs as part of its effort to deal with its large budget deficit, which is now estimated to be $310 million over the next four years.