Toby Levine braced for noise and pollution 10 years ago when she moved into San Francisco’s Mission Bay neighborhood, two blocks away from the Caltrain station at Fourth and Townsend streets.

Yet the pervasiveness of the diesel dust surprised her. It frosted the geraniums on her balcony and caused the leaves of the podocarpus trees to droop and turn brown. It stuck to her windows, freckled her neighbors’ deck furniture and collected in air vents.

“It wouldn’t be so bad if we were dealing with a less-dangerous chemical, but diesel is poison,” said Levine, who for years has led a neighborhood campaign to get Caltrain to minimize the emissions from its locomotives while neighbors wait for the rail system to go electric in 2022.

At the San Francisco station, which has 12 tracks, the first trains start rolling around 4:10 a.m. every weekday, and the last one pulls in at 12:05 a.m. During the slower-paced weekend schedule, trains run from 8 a.m. until midnight.

So for much of the week, diesel wafts through the air up to 20 hours a day in a booming new neighborhood. Plus, Caltrain’s fleet is more than 30 years old — “near the end of its life span,” said spokesman Dan Lieberman — and its engines don’t burn fuel that efficiently.

To further complicate matters, there are no state or federal laws that regulate idling diesel locomotive engines, so neighbors have depended on the rail line and its contracted manager, TransitAmerica Services, to write their own rules.

Caltrain’s manager of rail operations, Ben Burns, said the agency developed a strict protocol in February, partly in response to complaints by neighbors. The 29 passenger trains all have technology installed to turn off their engines automatically for layovers of more than 20 minutes, provided that the outside temperature, battery voltage and engine pressure are at levels that allow the trains to restart. Engineers are also required to shut trains down and hook them up to electricity if a layover is expected to exceed one hour.

“From a monetary standpoint, we don’t like trains sitting around and idling for no reason,” Burns said. “That’s money wasted for us.”

Burns pointed out that trains can burn through 10 to 20 gallons of fuel — up to $45 in taxpayer money — for every hour they spend parked with their engines running.

The protocol impressed Bruce Agid, who bought a condominium at 300 Berry St. in 2009, with a deck overlooking the rail yard. He said that after years of complaints and community meetings, the trains appear to be idling less.

“I think they’re being sincere,” Agid said.

Others are more skeptical.

Mike Cheney, a retired trainer for the diesel division at San Francisco’s Muni, noted that the protocol is voluntary and subject to human vagaries.

“They have the technology,” Cheney said, “but if the engineers don’t turn it on, there’s no punishment.”

As the rail system inches toward its goal of electric power, some neighbors are getting impatient. Smoke-belching trains weren’t such a big deal when Mission Bay was an industrial hinterland, but now the area is booming. Since 2000, developers have quilted the once-deserted terrain with 24 residential buildings and nearly 5,500 residential units.

“Now that there are thousands of people living here, it’s quite a bit more bothersome,” said Darren Orgel, who lives in Agid’s building. “If they can’t switch to electric for five years, maybe they should have come up with a way to get cleaner engines.”

Before moving to 300 Berry St. in 2013, Orgel lived for six years in an apartment at 260 King St., across from the train station. He said so much soot blew in that the vents in his ceiling turned black.

The most recent figures available from the Bay Area Air Quality Management District — a map based on 2010 data — show air pollution is higher in the South of Market and Mission Bay areas than in other parts of the city. Caltrain, diesel trucks and construction equipment are all major contributors, said air district spokesman Tom Flannigan.

Supervisor Jane Kim, whose district includes SoMa and Mission Bay, said she’s witnessed several neighborhood battles over air quality — a widespread concern when condo buildings are sprouting up next to train stations and freeways.

“There was a similar issue when we built housing by the Bay Bridge,” said Kim, whose staff has attended every community meeting about Caltrain. “For me there are ethical questions about building in certain areas. But that being said, we’ve built this neighborhood in Mission Bay. And then we pushed hard for electrification.”

Concerns over fuel emissions compelled the air district to award Caltrain $20 million in 2015 to help build the electric system.

That effort is under way, and to old-timers like Levine, it can’t happen fast enough.

“I’ve been hearing about electrification for 10 years,” Levine said. “My feeling is that Caltrain should be doing the best it can for the thousands of people that live here now.”

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