Caltrain officials on Thursday proposed closing up to 16 stations in Santa Clara and San Mateo counties — turning half the rail line’s stops into ghost depots, stranding thousands of riders, and leaving several huge shopping and housing centers without their prized train stops next door.

The plans, unveiled at a Caltrain board meeting, come in addition to a fare hike and deep cuts first revealed last year, including eliminating all but weekday rush-hour service between San Francisco and San Jose.

Caltrain leaders said the station closures and service cuts will be necessary starting July 2 to survive a record $30.3 million deficit — about one-third of Caltrain’s operating budget — unless they receive an influx of last-minute funding from outside sources, which they say is increasingly unlikely. The board does not expect to make a decision on the cuts until April.

“We have a very serious financial crisis looming,” said CEO Mike Scanlon. “I think we’ve looked under every rock” for more money.

Officials said for the first time Thursday that they are considering a 25-cent increase to all one-way fares, with corresponding increases to day and monthly passes. That would follow a 25-cent-per-zone fare increase that took effect last month, which amounted to a 7.2 percent bump for the average rider.

Officials now propose terminating service at as many as seven of these 10 stations: Bayshore in Brisbane, South San Francisco, San Bruno, Burlingame, Hayward Park in San Mateo, Belmont, San Antonio in Mountain View, Lawrence in Sunnyvale, Santa Clara and College Park in San Jose.

Proposals released earlier included ending all service south of San Jose Diridon Station, which would eliminate six stations, from Tamien to Gilroy. And proposals to end weekend and special-event service would close three more stations: the Stanford University stop, which is used only during football games, and weekend-only stations at Atherton and Broadway in Burlingame.

Still, based on a recent outcry about the cuts, Scanlon said he is optimistic the agency can find long-term funding — perhaps through a new regional tax — to eventually reopen stations and resume full service.

City leaders said the closures would be a big blow to their local economies and limit the ways residents and workers get around. They also complained that they have built or are planning large developments around the stations specifically to take cars off the road.

San Mateo officials just approved two of the city’s most ambitious commercial developments in memory next to the Hayward Park station, largely because they envisioned at least one-fifth of the workers riding the train. Mountain View leaders have endorsed a plan to build hundreds of apartment units and several shops next to the San Antonio station.

Meanwhile, the agency is building a new San Bruno station as part of a $147 million project, but under the proposal it would never open. Burlingame would lose service at its historic downtown depot, perhaps the city’s most recognizable landmark. Santa Clara, one of only a few cities in the Bay Area with more than 200,000 residents and workers combined, would lose its only train station.

In all, the worst-case scenario calls for trains to serve just half of the rail line’s 32 stops.

Caltrain riders reacted with dismay and fear that the proposed cuts will force them off the train.

“This is disastrous,” said Jessica Jenkins of Redwood City, who is legally blind and cannot drive. “Caltrain is a vital resource for people with disabilities like me.”

She rides the train frequently during noncommute times and at night for her work as a tutor and legal fellow at a nonprofit legal services organization.

“I understand that we are in a terrible economic situation in California,” she said, “but budgetary decisions should not be made on the backs of the disabled and otherwise disadvantaged. I hope that the decision makers do everything they can to avoid these terrible service cuts.”

Michelle Cook of San Jose and her husband ride Caltrain four days a week to their jobs at Stanford.

“If they were to do away with the College Park station, I would have to drive to Diridon to take trains to work at Stanford,” she said. “If both College Park and Santa Clara were removed from the schedule, I would be very hard-pressed to take the train as often as we do now.”

Closing College Park would also affect 175 students and faculty members who ride the train each day to Bellarmine College Preparatory.

Donna Johnston-Blair, who for 10 years has ridden the train from Palo Alto to her job teaching accounting at Santa Clara University, said she was distraught. “I love Caltrain,” she said.

All the proposed cuts would be necessary to erase the deficit, and even that may not be enough, officials said.

The stations slated for closure were chosen because they are not used heavily, and several rush-hour trains skip them to save time. About 13 percent of the agency’s 40,000 daily riders board at the stations proposed for closure. Officials have not yet estimated how many total riders they would lose from shuttering the stations.

Still, they serve thousands of commuters and casual riders, and the stations often represent an important link to nearby communities.

Belmont City Councilwoman Christine Wozniak said it would force many residents and workers in her city to abandon transit and hop in their cars.

“We have a lot of very loyal commuters who have really bent over backward to continue using public transit, specifically Caltrain, and this would be a huge problem for many of those people,” said Burlingame Mayor Terry Nagel.

Contact Mike Rosenberg at 650-348-4324 or mrosenberg@bayareanewsgroup.com.