It was too early to know the full extent of the storm surge and the damage it had caused early Friday, in part because several gauges had stopped working, said Parks Camp, a National Weather Service meteorologist in Tallahassee. Water level recordings in Steinhatchee, for example, rose rapidly until the gauge stopped working just before midnight, he said.

But it was clear that Helene had broken storm surge records across Florida’s Gulf Coast, many of which were last set in August 2023 when Hurricane Idalia drenched the same area. The Alafia River, which flows into Tampa Bay, peaked at 9.4 feet shortly after midnight, nearly three feet above the record set last year.

Storm surge — the rise in water levels caused by strong winds pushing ocean water ashore — is the leading cause of death from hurricanes, according to the National Hurricane Center. Rainfall, tides, waves and freshwater flow can contribute to the total rise in water level.

The surges can happen rapidly, sometimes leaving no time to act for people in their path. Just six inches of fast-moving floodwater can knock over an adult, the center said. It takes two feet of rushing water to carry away most vehicles, including pickups and S.U.V.s.

Storm surges can also erode beaches and coastal highways. Buildings that survive the winds of a hurricane can be damaged if their foundations are undermined by erosion.

With Helene, the threat of storm surge was the most serious along the Big Bend coast, where surges were expected to peak at 15 to 20 feet. But a storm surge warning was in place for nearly all of Florida’s western coast.

Water levels were expected to come down slowly Friday morning, but they were unlikely to return to normal levels by the time people wake up, Mr. Camp said. He urged people to wait until the waters recede and to beware of downed power lines.

On Thursday night, hundreds of people called 911 for help evacuating their homes in areas flooded by storm surge, which was expected to linger into Friday, the Pinellas County Department of Emergency Management said.

Some evacuated their homes. Bradley Tennant, 43, trudged out of his home in St. Petersburg and navigated flooded streets on Thursday. At night, he and his family watched their home flood through their security cameras, he said.

In Tampa, there were 78 evacuations and water rescues overnight after storm surge from Helene caused heavy flooding, according to the city.

Near Old Tampa Bay, Mark Hoffert, 53, who had initially planned to stay in his mobile home with his son, decided to leave after waters slowly crept into his living space, rising to six inches high.

Outside, he waded barefoot through chest-deep waters in the darkness to get to his neighbor’s car, which was parked on higher ground, and drive away. But, he said, his son stayed behind.

“I told him I wanted him to get out,” he said. “But he’s 20 years old. What can I do?”

But on Labor Day last year, what was meant to be a celebration of a new addition — a furnishings store — became a dash to prepare for a hurricane. Idalia had arrived.

“So, instead of getting ready to open, we started packing up,” Ms. Allen said.

After recovering from Idalia, Ms. Allen said they had been more prepared to handle Debby, which came ashore last month and fortunately spared the historic buildings. But as prepared as she can be, Ms. Allen expressed uncertainty in the hours ahead of Helene’s landfall.

“Now there’s this time of waiting and watching,” she said. “My mind has already started the process of: ‘What are we going to come back to? What are we going to see?’ My hope is that those buildings will be there. But I’m just not sure at this point.”

These hurricanes are not Ms. Allen’s first experience with tropical storms in Cedar Key. When she moved to the island community, as her husband was still building the biological station, Hurricane Hermine hit late at night in August 2016. She wasn’t sure she could stay. Then she saw the community rally. She saw Cedar Key repair itself. And that still resonated on Thursday while she was hunkering down in Gainesville.

“My heart and my soul is in that little community,” Ms. Allen said.

She said she and her husband know the risks they face to live on the Gulf Coast.

“Part of the process is getting my mind to: ‘Here we go again. We’ve got to do it again,’” Ms. Allen said. “When we see people who have been in Cedar Key for a long time — they’re so resilient. They’ve shown us how to do it. Ever since Hermine, we’ve seen it. And we asked them, ‘How does it get better?’ But we watched it get better.”

Friday: The storm quickly follows Interstate 75 north out of Florida.

The storm is expected to move very quickly overnight, reaching north Georgia by Friday morning, and the worst will be quickly over in Florida. But this storm’s quick pace will mean the core of its most intense winds could extend all the way to near the Atlanta metro area.

Because of the vast size of Helene, the tropical storm-force wind gusts are also likely across Georgia and the Carolinas late Thursday and into the day Friday, particularly over the higher terrain of the southern Appalachians.

Even worse is the heavy tropical rainfall tied up in the storm, which will push further into the Appalachian Mountains, where the National Weather Service has warned the storm will be one of the most significant “in the modern era.”

For the third day in a row, from foothills in Atlanta to mountains in Asheville, where rivers and creeks are already pushed to the brim, even more extreme rain is expected to fall on Friday.

The combination of the wind and the wet soil will make it much easier for trees to fall. And it makes the rough terrain susceptible to landslides.

As Helene moves north, it will begin to spin around another storm system, which will make it turn left over Tennessee.

This weekend: The remnants of the storm will linger

Rain will fall across central Kentucky and Tennessee eastward to the central Appalachians and Mid-Atlantic region the remnants of Helene combine with another weather system.

This rainfall could result in more flooding as the rains persist through Monday.

Among the city’s notable trees is the Lichgate Oak, an ancient tree that has become a natural landmark. The city is also believed to be the home of two “Moon Trees” — a sycamore and a loblolly pine — grown from seeds taken into space during the Apollo 14 mission in 1971.

However, the very trees that shape Tallahassee’s character could become a hazard during the storm. A city report on its urban forest warns that much of the city’s trees are short-lived and have wood that is prone to breakage under stress, making them particularly vulnerable to strong winds.

Helene could test this vulnerability. Though Tallahassee is located at least 30 miles inland, the city is under a rare hurricane warning. Forecasters have warned that the storm could bring gusts of up to 75 miles per hour, and potentially stronger winds exceeding 110 m.p.h. The city has never before recorded sustaining hurricane-force winds.

Brenda Geddes, 60, a longtime Tallahassee resident who was stocking up at a Walmart on Wednesday in advance of the storm, said of the trees, “When it’s a storm like this, you can only do so much.”

In past hurricanes, the city has largely been protected from strong winds because of its geography, but storms have still caused significant damage outside the city.

Donna Staab, 67, who lives about an hour and a half southeast of Tallahassee in Keaton Beach, recalled how Hurricane Idalia last year felled over a dozen trees on her neighbor’s property and a few on her own. The sound of wood chippers became a familiar backdrop.

“You could hear it for weeks afterward,” Ms. Staab said.

The fear of similar destruction is weighing on Tallahassee residents such as Natasha Sutherland, 39, who, along with her husband, decided to head to Alabama for safety on Wednesday. As she drove north, she became emotional while taking in the view of the city’s overhanging trees and her favorite places.

“I started crying a little bit,” she said, as a thought occurred to her: “‘Gosh, this might be the last time I see it like this ever again.’”

Last year, researchers at Columbia, Harvard and the U.S. Federal Reserve Board sounded the alarm about Florida and the home insurance industry. In a paper, they warned that the stability of Florida’s insurers was worse than it seemed, because those insurers appeared to be getting inflated scores from the company charged with evaluating their financial health.

“Our research shows that Florida’s property insurers are far more vulnerable than people might think, with insolvency potentially in the cards,” said Parinitha Sastry, an assistant professor of finance at Columbia Business School and one of the paper’s authors.

The researchers warned about a specific scenario: A big storm hits Florida, causing a tidal wave of insurance claims. Insurers that looked stable on paper start to fail, preventing them from paying out claims to homeowners. That in turn drives up the number of homeowners defaulting on their mortgages because they can’t afford to repair their homes.

At that point, what started as a Florida problem becomes a national problem. The organizations that buy most U.S. mortgages, Fannie Mae and Freddie Mac, are backed by the federal government. If Florida homeowners start defaulting on their mortgages, Fannie and Freddie stand to lose money — and those losses could get passed on to federal taxpayers.

“Our research shows that the financial costs of fragile insurers go well beyond the borders of Florida,” said Ishita Sen, an assistant professor at Harvard Business School and another of the paper’s authors. She said the insurance requirements imposed by Fannie and Freddie are poorly designed.

The stakes could be gigantic, Senator Sheldon Whitehouse, a Democrat and chairman of the Senate Budget Committee, warned this summer as he made a comparison to the 2008 financial crisis.

“Who will be left holding the bag?” Mr. Whitehouse said during a hearing in June on climate change and insurance markets. “The federal budget takes a hit because these insurers and their policies are accepted by Freddie Mac and Fannie Mae, who either own or guarantee a large part of our $12 trillion mortgage market.”