When the rain began to pour over Green Mountain, N.C., in late September, Alison Wisely kept a close eye on the puddles growing slowly outside her window.

Hurricane Helene was churning across the American South, and Ms. Wisely, 42, and her fiancé, Knox Petrucci, 41, were hunkering at home with her two young sons. The house was hundreds of miles from any coastline.

On the morning of Sept. 27, a nearby river overflowed, and catastrophe came quickly. Floodwaters rushed toward the couple and the children — Felix, 9, and Lucas, 7. In a frantic effort to escape, all four lost their lives.

Their deaths represent only a small fraction of Helene’s terrible toll. The storm has killed more than 200 people, making it the deadliest tropical cyclone to strike the mainland United States since 2005.

Over the last three months, The New York Times collected data on Helene’s deaths from county coroners and state officials, and interviewed family members.

The findings revealed that rain, which led to flooding and landslides, was the most deadly part of the storm, followed by wind, which toppled trees. And they showed that most of the deaths happened in counties where the risk of hurricane fatalities had been considered low, according to data from the Federal Emergency Management Agency.

The deaths from Helene show how hurricane mortality has changed. Historically, most of the immediate deaths associated with major hurricanes in the United States have been caused by storm surges in coastal communities, according to data from the National Hurricane Center. But in the past decade, freshwater flooding has become even deadlier.

Helene also showed that indirect deaths — caused by things like power outages and traffic accidents, often after the storm is over — were distressingly common. At least two dozen people died from Helene-related causes in October, days after the hurricane had passed.

Freshwater flooding in North Carolina and Tennessee

Hurricane Helene was deadliest in North Carolina, where it killed more than 100 people. And at least 17 people died in Tennessee, including six who had been working at a plastics factory in the town of Erwin, just across the border. Search and rescue teams worked to recover the remains of victims who may have been swept across state lines by floods and landslides.

In Green Mountain, where Ms. Wisely and Mr. Petrucci lived with her two boys, the threat did not seem severe at first, said Lance Wisely, Ms. Wisely’s former husband and the boys’ father.

But when the nearby North Toe River burst from its banks and the water began to rise, neighbors saw Ms. Wisely and Mr. Petrucci put the children in the car in an attempt to flee, Mr. Wisely said.

A rush of water carried them all away. All four were buried together on Nov. 9, the same day that the couple were meant to be married. “I wish that I could have protected them from this,” Mr. Wisely said.

National Hurricane Center data suggests that the rain associated with major storms has become more deadly than storm surge, partly because storm surge preparation has improved in coastal areas, said Michael Brennan, the center’s director. Hurricanes also tend to be wetter in a warming world, which can lead to more freshwater flooding. Climate change could make flooding deaths even more common.

Falling trees in Georgia

In Georgia, the main cause of death was not flooding but wind.

At least three dozen people died in the state, mostly because of trees toppling onto homes and vehicles, according to reports from officials. Helene entered Georgia as a hurricane but left as a tropical storm, with winds around 70 miles per hour.

Many residents had not been prepared for such strong gusts so far inland.

In Thomson, Ga., a small city west of Augusta known for its flowering Camellia plants, Mary Ann Jones stayed in the two-bedroom mobile home she shared with her daughter, Kobe Williams, and her 1-month-old twin grandsons, Khyzier and Khazmir.

Shortly before sunrise on Sept. 27, Ms. Jones, 55, heard a whoosh of wind. Suddenly, she saw tree branches extending from her daughter’s bedroom. She screamed out for her daughter, but there was no answer.

When the emergency responders arrived, they told Ms. Jones that her daughter and grandsons were dead.

“Everything in the house reminds me of my daughter,” she said. Ms. Williams delighted in her sons, her mother said, and insisted on dressing them differently so that each could grow into his own person.

Unlike storm surges, falling trees can be difficult to predict and even more difficult to evade, Dr. Brennan said. “It’s a different type of problem that we need to think about.”

A fatal surge in Florida

Florida, by contrast, confronted a familiar threat. In the days before the hurricane walloped the gulf coast with 140-mile-per-hour winds, state officials sent evacuation notices to the areas in harm’s way.

The evacuations appeared to have saved many lives. Still, at least 21 people died in Florida, mostly from the storm surge.

As Helene approached the Big Bend region of the state, Marjorie Havard, 79, told her older sister on the phone that she thought she would be safe in her home about 200 miles south in St. Pete Beach.

The sister, Marcia Napier, 81, said she had urged Ms. Havard to join her farther south, in Venice, “but she said, ‘Oh, I’m just going to ride this one out.’”

The next morning, Ms. Napier called her sister over and over again. But no one answered. Later, she learned that Ms. Havard had drowned in the salty water that had rushed into her single-story home overnight.

Ms. Havard, who grew up on a farm in Ohio, raised her children before she became a carpenter and traveled the country repairing nuclear cooling towers.

Ms. Napier tries not to think about her sister’s final moments. Instead, she remembers her adventurous life, and the way the two of them — both widows — had supported each other. “I feel like there’s a void in my life,” Ms. Napier said.

Deadly damage in South Carolina

As in other states, Helene’s wind and rain were fatal in South Carolina. But the deaths there also showed how storms could kill even after the skies cleared.

Coroners’ reports suggest that of the more than 50 fatalities in the state related to Helene, at least 10 were because of traffic accidents and medical emergencies after the storm, prompted by power outages, infrastructure damage or the physical strain of cleaning debris.

On Oct. 1, two sisters from Union. S.C., left their home for a cardiology appointment. It was a few days after Helene had passed through and the siblings, Faye Farr Webber, 87, and Sarah Ann Farr, 77, had thought the worst of the storm was over.

Ms. Webber’s daughter, Angie Padillo, had been driving the sisters to the appointment when she pulled up to an intersection in Spartanburg County. Because of Helene, the traffic lights were not working.

Ms. Padillo, 60, treated it as a four-way stop, but another vehicle did not. Their Toyota Camry was struck by a sport utility vehicle, Ms. Padillo said, killing both her mother and aunt.

Ms. Padillo was hurt, too. She is still recovering from broken ribs and a brain injury as she grieves the loss of her mother, with whom she used to speak every day on the phone, and her aunt, whose laughter had been a constant source of joy.

The long tail of trouble

In the days after a storm, keeping track of the death toll becomes a tricky endeavor.

Officials have to make grim judgment calls about which fatalities can be attributed to the storm: Would this man have died of cardiac arrest if he had not been lifting tree branches? Could that woman have survived if a power outage had not interrupted her dialysis session?

Some data suggests that hurricanes can cause deaths weeks, months and even years after they hit.

A paper published in the journal Nature in October shows that tropical storms in the continental United States have taken a hidden toll. Looking at hundreds of events from 1930 to 2015, researchers found that the average tropical storm resulted in an additional 7,000 to 11,000 deaths over the 15 years that followed.

The causes of those deaths are wide-ranging. The stress of a major weather event can exacerbate long-term health problems, for example. Storms can drain the resources of local governments, making it harder to pay for firefighting or road repairs.

In the immediate aftermath of a storm, older people and people with disabilities are more at risk.

But when it comes to long-term fatality risks, different patterns emerge. Infant mortality appears to grow, the Nature study found. Communities with a majority Black population fare worse than majority white areas long after powerful storms.

The data suggests that Helene could cause 44,000 to 68,000 extra deaths over the next 14 years, said Rachel Young, an environmental economist at the University of California, Berkeley.

The ability to address these risks, which are partly the result of wealth disparities, may fall beyond the remit of meteorologists and emergency managers.

One solution, Dr. Young said, would be to direct more resources toward those communities that tend to be hit harder over the long term. “There’s a need to focus not just on repairing physical property damages,” she said, but also on long-term health care services.

In the short-term, addressing freshwater flooding presents a unique challenge, because rain is not confined to any particular geographic area.

“We have to build up the infrastructure around freshwater flooding and the response to it, to try to start to approach what we’ve done with storm surge,” Dr. Brennan said. “And that’s not going to happen overnight.”