It’s not just faulty lines and failing cars. The MBTA has a climate problem.

Flood barriers enclosed the entrance to the Aquarium subway station last year.Michael Dwyer/Associated Press

INTO THE RED: Climate and the fight of our lives

If you think the T is in trouble now, get ready.

By the end of this decade, a new study finds that flood damage to the T will cost tens of millions a year as sea levels rise and storms become more intense and frequent, according to the authors of the report in the journal Communications Earth & Environment.

“The MBTA really needs to do something,” said Michael Martello, a researcher in MIT’s Transit Lab and lead author of the report, which was partially supported by the MBTA. “Our analysis shows that their inaction has already doubled their risk and is expected to double it again if nothing else is done.”

Even now, with the sea level around Boston about a foot higher than it was a century ago, major storms have caused flooding in the Green Line near Fenway Station and at Aquarium Station on the Blue Line. But as seas rise another 1.4 feet by 2050, as NOAA has projected, even a relatively mundane storm — the kind that hits every two years — could cause massive damage to the T, inundating vast portions of the system, according to the study.

Without adaptation measures, the cost of keeping up with the damage will more than double from $24 million in 2020 to $58 million by 2030, the study estimates. And it will get worse from there. Depending on how much seas rise — a result of how aggressively the world responds to climate change — annual costs to the T at the end of the century could be $1.2 billion or, in an extreme scenario, $9.3 billion, according to the study.

The study, published last week, lays bare yet another expensive headache for an agency already struggling to provide safe, reliable transportation while updating aging cars, tracks, and other critical equipment. Making the stakes even higher in coming years, city and state climate plans are counting on a high-functioning subway system to lure drivers off the road and slash emissions from gas cars.

Martello’s analysis builds on a study he published in 2021 that found a 100-year storm — one that has a 1 percent chance of occurring in a given year — would completely inundate the Blue Line and large portions of the Red and Orange lines in 2030, and that by 2070, nearly the entire network would be flooded by such a storm.

Joe Pesaturo, a spokesman for the MBTA, said the research is one of the tools the agency will be using to assess impacts from climate change. “This report directly informs the MBTA’s work regarding tunnel portal flood protection,” he said, adding that the MBTA is participating in various regional partnerships as well as the Statewide Hazard Mitigation Climate Adaptation Plan, a process launched in 2018 to incorporate climate impacts and adaptation into planning.

Martello said the MBTA has made an important change since he concluded work on the study, installing flood-proofing barriers around the four entrances to the Blue Line’s flood-prone Aquarium Station — a $1.7 million project.

He said the measures hold an important lesson for the MBTA: A yet-to-be-published analysis he performed after the barriers were installed estimates that flood damage costs dropped to a projected $18 million in 2023 and to $39 million by 2030.

That analysis shows just how much money smart adaptation measures can save the system in the long run, Martello said. He’s hoping his study can be used to help the MBTA prioritize and justify taking these steps now, even as it juggles pressing needs across the system.

Still, he said, those costs — and the risk of the system being disabled — should be a wake-up call, especially because as the sea level rises, so does the likelihood that a climate-fueled extreme storm will hit Boston.

Kate Dineen, president and CEO of A Better City, a transportation-focused business group, called the findings “sobering, but not surprising.” Dineen, who helped lead New York state’s response to Superstorm Sandy, said she felt the MBTA is well-positioned to act with urgency.

“It is time for the agency and our Commonwealth to transition from planning to implementation and prioritize the adaptation projects needed to fortify our vulnerable transit system against worsening flood and heat impacts,” she said.

Pesaturo, from the MBTA, said that some of that work is already underway, and that this report will help direct their effort.

According to the MBTA’s Proposed Capital Investment Plan, the agency has several flood-related projects planned starting in 2024, including $50.3 million for flood mitigation in tunnels and $21.1 million for new headhouses at the Silver Line’s Courthouse Station, which will include flood control barriers.

Other projects, including floodgates and large steel doors at the entrances of the Green Line tunnel near Fenway Station and the development and implementation of flood prevention measures on the Blue Line, are completed or near completion, according to the plan.

It’s welcome work — if a little late, said Paul Kirshen, a climate scientist from UMass Boston who studies sea level rise and who was on a team that reviewed and approved Martello’s work. “This should have been done earlier,” he said. “Anything new that’s been built since about 2000, they should have been thinking about climate change.”

Going forward, Kirshen said, he and others in the scientific and advocacy community are hoping to see more regional approaches to adaptation that could benefit not just one agency, but meet needs across the vulnerable locations in the city.

“That’s great that an agency or some building owner is protecting their own assets, but that means that after a storm, that asset will still be standing but it doesn’t mean people will be able to get there,” he said.