After weeks of warning, the time has come. All day Saturday and Sunday, BART will close the Transbay Tube for major track repairs, severing the regional transit system at its backbone and forcing riders onto buses and ferries or into their cars to get between San Francisco and the East Bay.

The shutdown underscores the wear and tear of an aging system that is more popular than ever, and raises questions about whether agency leaders could have done anything to avoid taking the tube offline for a full weekend. But mostly, it’s a serious headache for riders.

BART will open for business on Saturday and Sunday, but the stretch of track reaching from downtown Oakland to the Embarcadero Station — including the Transbay Tube and West Oakland station — will be closed. The shutdown will be repeated over the three-day Labor Day weekend.

To keep the Bay Area connected, BART will run continuous bus service between downtown Oakland and downtown San Francisco, and ferry service is also being increased. But BART officials warn that delays could add an hour or more to journeys, and traffic across the Bay Bridge, always clogged on weekends, is sure to be a mess.

Their advice? Stay on your own side of the bay.

“We know we’re going to inconvenience a significant number of people, and the fact is we need to inconvenience people to get the work done,” said Jim Allison, a BART spokesman. “When you need to take the bandage off, you need to do it quickly and let the healing begin.”

Organizers of Oakland’s Art and Soul Festival, which takes place both days this weekend, were among those distressed when they first learned of the closure — especially since BART is a longtime sponsor.

But they said they were heartened that the transit system will run more frequent trains on both sides of the bay, and that the bus service will still give San Franciscans a way to get to the festival, which features music and arts on a number of stages.

“It’s a little unclear what impact it will have,” said Samee Roberts, the festival’s executive producer and founder. “But we have a great festival, we’ve been around 15 years, and we hope that enough people know that and will make the trek.”

While the busiest part of the BART system is closed, the overhead tracks through West Oakland, and the tube itself, will be swarming with activity. The reason for the closure is the need to replace a set of crossover tracks, a system of switches and rails that allow trains to change directions or steer around stalled trains.

The crossover, between the West Oakland Station and the tube, is part of the original system and is nearly 45 years old, said Tamar Allen, BART’s chief maintenance and engineering officer. The wooden ties are rotting, and the sections of rail and the equipment that lets trains change tracks are wearing down.

The deteriorating conditions have already forced BART to slow trains speeding toward the tube and to stop using the crossover, which has contributed to longer delays.

BART could put off the work but would run the risk of an immediate shutdown for emergency repairs within three years, Allen said during an online BART town hall meeting where officials fielded questions from the public.

“This is not emergency work,” said Alicia Trost, a BART spokeswoman. “It’s planned maintenance, but we can’t do it during the nightly maintenance window” — a two-hour period when trains aren’t running and the power is shut off.

About 90 workers — BART’s entire track maintenance crew — will work around the clock to rebuild the crossover, also known as an interlocking. They’ll replace 932 ties as well as four switches and 2,400 feet of rail over a nearly half-mile stretch of track. Every piece of heavy equipment, from track grinders and flat cars to trucks that can roll on the rails, will be pressed into service.

BART studied ways of completing the work without a weekend shutdown, but the narrowness of the aerial structure, and the type of equipment needed, made it impossible to get the job done during the few hours that BART is powered down, Allen said.

“We have, over the years, tried many ways to mitigate the wear and tear on these interlockings without shutting them down,” Allen said. “If we want to provide a railroad for our customers that is good for another 35 to 40 years, we need to bite the bullet and shut it down.”

While the system is shut down, BART will also perform maintenance work in the Transbay Tube, inspecting the tracks and power cables, cleaning third-rail insulators, replacing some worn rail and cleaning trackside train-control equipment that is often the cause of delays.

“We don’t usually get this much time to work in the tube,” Trost said, “so we have to take advantage of it.”

While the crews are at work, BART riders hoping to cross the bay will have to catch buses between Oakland and San Francisco.

BART has contracted with a host of Bay Area transit agencies to run a fleet of 94 buses from the just outside the 19th Street Station to the temporary Transbay Terminal in downtown San Francisco, two blocks from the Embarcadero Station.

Passengers who don’t want to make the walk can catch a free ride on a Muni bus to the station. BART will also run a free shuttle between the West Oakland and 19th Street stations.

Buses are scheduled to leave about every 45 seconds if needed. Since BART hauls about 98,000 passengers across the bay on an average Saturday, and 80,000 on a typical Sunday, they will most likely be busy. To speed buses across the Bay Bridge, the agency has arranged for dedicated on-ramps and off-ramps as well as control of metering lights.

Replacing the crossover is expected to cost about $2 million, not including the $1.5 million price tag for the bus shuttles — and still-undetermined costs of lost revenue.

BART officials say it will be worth the cost. The work not only will get the crossover in shape for the next three to four decades, but it also should immediately deliver a smoother and slightly faster ride and reduce the length of delays. While most of the job will be done by the end of Labor Day weekend, some work will continue at night until January.

Still more crossover work — and likely service shutdowns — are down the track. BART is already making plans to replace crossovers between the San Leandro and Bay Fair stations and the Balboa Park and Daly City stations.

BART Director Tom Radulovich said the weekend closures may be painful but show that the agency is paying attention to the oldest and busiest parts of its system.

“We’re in a better place,” he said. “It’s a sign that we’re taking maintenance more seriously.”

Michael Cabanatuan is a San Francisco Chronicle staff writer. E-mail: mcabanatuan@sfchronicle.com Twitter: @ctuan