Millions of Americans will venture out to buy a live Christmas tree this weekend—though growers are having to overcome historic challenges to get them to the lots.

Root rot. Scant labor. Foreign competition. Inflation on everything from seeds to tractors. And that was before Hurricane Helene wreaked havoc on the western part of North Carolina, which produces more Christmas trees than any state except Oregon.

“It’s the hardest year ever in North Carolina agriculture,” said Lee Wicker, deputy director of the North Carolina Growers Association. “The damage from Helene had a compounding effect. It wasn’t one single thing, it was all these things that happened.”

Roughly 21.6 million real Christmas trees were purchased in the U.S. last year at a median price of $75, according to the National Christmas Tree Association. Historically, the day after Thanksgiving is the peak sales day for live trees. But Thanksgiving comes late this year, making for an unusually short selling season, another pressure on growers.

Delivering one of the most popular Christmas tree varieties, Fraser firs, to tree lots in recent weeks fulfilled the Christmas wish of many North Carolina growers. One out of four Fraser firs sold nationally—and virtually all Fraser firs sold on the East Coast—comes from western North Carolina. The area was devastated by flooding that left 95 people dead, washed out roads and destroyed homes, including that of tree farmer Waightstill Avery III.

Avery, 58, also lost a barn, an office, hauling trailers, dump trucks and—worst of all—60,000 trees, a third of the total at family-owned Trinity Tree Company-Avery Farms. Many of the damaged trees were partially submerged by floodwater. Others were covered in clingy silt that resists washing. Avery’s staff, which includes his adult sons, have been recovering what they can, cutting tree tops off for table displays and using any salvageable greenery to make 3,000 wreaths, twice the normal number.

“We’re cleaning what we can out and we’re making little 4-foot trees out of 8-foot trees,” Avery said. “You had to salvage something.”

Not all farms were hit hard. Fraser firs, prized for their green bristles with silver undertones, bright fragrance and excellent needle retention , grow at high elevation, so most were planted at some distance from streams and riverbeds. Still, flooding blocked roads, stranded loved ones and damaged homes and businesses.

The North Carolina Christmas Tree Association said there should be enough supply for anyone who wants a real tree this year, though growers say that buyers might need to adjust their expectations. Some church groups that flock to the mountains to stock their tree lots back home have been intentionally seeking out scraggly “Charlie Brown” trees as a show of support. Some lots are offering tree buyers the opportunity to purchase a tree for a family in western North Carolina affected by the storm.

Helene’s impact will affect the Christmas tree industry for years to come. It takes roughly 10 years to grow a full-size Fraser fir, which grows about a foot a year. Many of the trees that were damaged were several years from maturity, pressuring supply in five or six years. Others were seedlings being closely tended to in a nursery for several years before being planted on a mountainside.

When the nursery at Barr Evergreens flooded, the family-owned business lost 200,000 seedlings, valued at $500,000. Unlike corn or soybeans, a crop of Christmas trees has a very long growing cycle, making it impossible to affordably insure, said Rusty Barr, the second-generation owner.

The storm made a difficult business even harder, Barr said. The Fraser fir thrives on the high peaks of the southern Appalachian Mountains, with their cool temperatures and plentiful rainfall. But rain has been unpredictable, not only from the roughly 10 inches of rain dumped by Helene but also by the frequent lack of it. A drought several years ago knocked out much of that year’s crop. There was a welcome early snow this year, though the area gets nowhere near the annual snowfall it did when he was young, Barr said.

Scant labor is also a problem. North Carolina is one of the biggest users of the H-2A visa program for agricultural workers. The regulations around hiring foreign workers have become increasingly cumbersome, said Barr, who typically employs and houses 35 workers from February until December, and brings in another 20 for the October harvest. The hourly rate he pays is increasing to more than $16 next year, another cost to absorb.

Barr, 56, said he supports the incoming Trump administration’s pledge to crack down on illegal immigration but is nervous about the rhetoric around clamping down legal immigration.

“We live in a community that’s mostly older people and retired people, and the labor force goes from 700 workers to 2,500 workers at harvest,” he said. “We couldn’t do it without them.”

Industry challenges are both external and from within, particularly with the proliferation of phytophthora, a root rot related to brown algae that is difficult to eradicate.

Like any agricultural crop, Christmas trees have weathered booms and busts. One of the biggest followed the 2007-09 recession when farmers planted fewer seedlings or went out of business altogether as consumers pulled back spending. That created a supply problem a decade later that led to price hikes.

The industry is also up against shifting consumer habits, such as some aging baby boomers’ preference to stop putting up live trees. There is increasingly stiff competition from China-made artificial trees, which have become easier to assemble and more lifelike, sometimes boasting scents like “white winter fir.”

Such challenges have buffeted market size: The number of trees harvested in the U.S. has declined 30% since 2002, according to the U.S. Agriculture Department, even as the American population has grown 16% over the same period.

Fifteen years ago, Barr harvested 90% of the trees he planted. Now it is 70%.

Still, he said he wouldn’t trade the work for any other. A Fraser fir has been selected as the White House Christmas tree 16 times, including this year’s from Cartner’s Christmas Tree Farm in Newland, N.C. Area growers said the honor had special meaning this year, a symbol of resilience and hope.

“It’s the Cadillac of Christmas trees,” Barr said of the Fraser fir. “You’re giving people the centerpiece of their home for the holiday season.”

Marc Ferguson, an emergency-services administrator from suburban Raleigh, purchased a live Christmas tree for the first time this year. Ferguson grew up with an artificial tree and had been using the same pre-lit one for the past 15 years.

“Last year the dog finally peed on it one too many times, and we had to throw it in the trash,” he said.

This fall, he brought donated baby supplies and EpiPens up the mountain for people in need after the hurricane. He and his family then decided to make the three-hour trek to Boone to pick out a real tree in a further show of support.

Ferguson enjoyed seeing other cars drive by with trees strapped to their roofs and expects the Christmas tree trip will become an annual tradition. “We went to the farm, picked one up and had a good time,” he said.

Write to Valerie Bauerlein at Valerie.Bauerlein@wsj.com