Leonard Brown was among the few people wandering around Powell Street BART Station on Wednesday morning with no protective garments.

While others wore masks, gripped grocery bags with surgical gloves or carried large bottles of Purell in their pockets, Brown stood out in his white T-shirt and jeans. His car had broken down, and he needed to take BART to run errands in downtown San Francisco. The coronavirus pandemic couldn’t stop him.

“I’m not about to sit at home and go crazy,” Brown said, shrugging as he sauntered over to the Richmond-bound platform.

He’s among the approximately 30,000 people who still take the rail system on weekdays — a drop of more than 90% from BART’s daily haul of 400,000 riders in February. Many of the passengers who remain are frontline workers who wear delivery uniforms or scrubs. Some rely on transit to go shopping or get to doctor appointments. A few who boarded trains and buses on Wednesday said they felt uneasy jostling among strangers, though others, like Brown, seemed resigned.

“I was really trying to avoid BART until after the pandemic,” said Felipe Lopez, who was dabbing on hand sanitizer as he waited for an East Bay-bound train from Powell. Lopez is unemployed and mostly stays home in Oakland, but he had to catch BART on Wednesday to pick up a package in San Francisco.

Although the Bay Area has shut down, some of its transit keeps running. Agencies have scrambled to redesign their systems on a dime, grappling with losses climbing into the hundreds of millions of dollars, but striving to serve passengers who have to get to work. Day-to-day problems with grime, transients and equipment have become magnified as transit takes on a more critical role for a small population.

And then there are the crowds.

“Oh yes, we have seen crowds — oh my goodness,” San Francisco transportation chief Jeffrey Tumlin said in an interview Wednesday. He noted that most surges occur when a bunch of shift workers leave a hospital at the same time and pile onto the same bus.

Tumlin’s staff monitors these swells from a command center on Market Street, where they constantly retool the system to keep riders 6 feet apart, while delivering reliable service. It’s a painstaking calculus, made more difficult by train operators calling in sick.

All of these complications came to a head two weeks ago. Working from home late on a Friday evening, Tumlin got a call from transit Director Julie Kirschbaum. Muni didn’t have enough operators to drive all the buses, she said. The number of riders had tanked overall, but a few essential workers still depended on public transit.

So in one weekend, Tumlin’s staff cut service down to 17 lines and effectively rebuilt a century-old transit system from scratch. They now keep track of how many people board each bus, using door sensors and assigning teams of fare inspectors to count passengers by hand. As the buses fill, drivers stop picking up riders. Muni has also shifted to headways instead of schedules, meaning drivers try to space the buses evenly apart, rather than arriving at each stop at a certain time.

Tumlin is testing another solution: sending yellow-vested ambassadors to bus stops to dissuade people from taking frivolous trips.

Crowds appear to be less of an issue for BART, owing to its sprawling size and the steep drop in riders. Facing losses of $37 million a month in fares and parking revenue, General Manager Bob Powers slashed service to two trains an hour this month. The move coincided with a shift in rush hour, which now lasts from 5:30 a.m. to 7 a.m., he said, instead of the normal 6:30 a.m.-to-9:30 a.m. peak.

That’s the result of who takes BART during shelter in place, Powers said: grocery store clerks, hospital employees, people who work in medical clinics. Even during the morning peak, passengers have enough space to spread out, he said.

“I have a team meeting every morning with my operations staff, and we look at heat maps” to show where people are boarding, Powers said. “We’re keeping an eye on social distancing.”

Most BART cars are eerily sparse. Some have enough passengers to cause discomfort. A train leaving MacArthur Station at 9:25 a.m. Wednesday morning had 19 passengers in one of its center cars, filling a seat in each row. A man boarded the train car at Montgomery Station and paced the aisle, approaching individual riders and asking for change.

Chase Bronson, a fire systems inspector who rides BART daily, is fed up. Sitting on a Richmond-bound train Thursday morning, he wore an N95 mask, blue surgical gloves and a gray uniform. Bronson lives in the Fillmore neighborhood and normally catches an early train at about 5:30 a.m. to start his 13-hour work day. Like many riders, he constantly worries about the coronavirus.

“I feel like there are a lot of germs on BART, period,” Bronson said. “And now it’s filthy,” he added, gesturing to a black smear on the train wall.

Powers is optimistic that he’ll eventually restore BART to full service. Tumlin has a more sober view. The San Francisco transportation czar predicts that Muni may emerge from this pandemic a completely different system. Like many government leaders, he sees the future through the prism of a global pandemic and subsequent economic collapse.

“We will likely lose $200 million this quarter,” Tumlin said. “The (federal) stimulus will cover some of that, but it’s anyone’s guess how long it takes the economy to recover.”

He added: “I don’t know that we will ever bring service back to the way it was six months ago” — a now-distant era when 720,000 people jammed cheek-by-shoulder into Muni’s subway and buses each weekday.

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