Photo: Santiago Mejia, The Chronicle

Tolls will go up $1 on seven Bay Area bridges Jan.1, raising the cost of crossing the Bay Bridge to $7 during peak hours, as other spans jump to $6.

It’s the first of three increases that voters approved by passing Regional Measure 3 in June. Additional increases will take effect in January 2022 and January 2025, at which point Bay Bridge motorists will shell out $9 apiece during rush hours to drive over the choppy waters that separate Oakland from San Francisco.

The new rates earned unanimous support from officials at the Bay Area Metropolitan Transportation Commission earlier this month, despite quibbles from a handful of Bay Area commuters. Some said the tolls put an unfair burden on the working class, while others expressed doubt that the commission would spend the money on the projects it had announced — such as BART’s extension into Silicon Valley and an intricate stitching of express lanes along the Interstate freeways.

Regional Measure 3 will inject $4.5 billion into Bay Area transportation systems, providing funds for 35 transit and road improvements intended to ease congestion, smooth bumpy pavement and get people out of cars. Officials hope to double the region’s ferry capacity, add track along the Sonoma-Marin Area Rail Transit line and extend Caltrain to the new Transbay Terminal.

“Here’s the good news: tolls are going up so that traffic can go down,” said Carl Guardino, chief executive officer of the Silicon Valley Leadership Group, which helped steer the campaign for RM3.

But those developments come with a price for drivers. Cars and trucks crossing the Dumbarton, Richmond-San Rafael, Antioch, Carquinez, San Mateo-Hayward and Benicia-Martinez bridges will pay $6 starting Tuesday, while Bay Bridge drivers will pay $7 at peak weekday hours, $6 on weekends and $5 during nonpeak weekday hours. Carpools, motorcycles and clean-air drivers will also see their discounted rates swell slightly, from $2.50 to $3.

Photo: Noah Berger / Special To The Chronicle 2017

Critics of the measure call it a tax, rather than a fee, and say it should have been required to pass by a two-thirds threshold — significantly more than than the 54 percent support it drew from voters. In July, the Howard Jarvis Taxpayers Association filed a lawsuit to stop RM3 on those grounds. It’s inching forward in San Francisco Superior Court.

David Schonbrunn, whose group Transportation Solutions Defense and Education Fund opposes the measure and toll hikes, characterized the transportation improvement plan as a ruse.

“When they say they’re going to fix traffic, we know there’s no way they can do that — or they would have done it already,” Schonbrunn said.

Tuesday’s increase is the first on state-owned bridges since 2010. It coincides with discussions to raise tolls on the Golden Gate Bridge, which could climb to nearly $10 by 2023.

Rachel Swan is a San Francisco Chronicle staff writer. Email: rswan@sfchronicle.com Twitter: @rachelswan