For all its beauty, there’s something unsettling about the landscape, something hard to ignore: hundreds of the trees growing along the water are dead.

Billy Reiter-Marolf, a wildlife biologist for the U.S. Fish and Wildlife Service, calls it the boneyard. It’s a popular spot for hunting, fishing and paddling, so people have begun to take notice of the abundance of tall, leafless stumps pointing to the sky.

“Visitors ask me, ‘What’s going on, what’s happening here?’” Reiter-Marolf said. “It just looks so bad.”

Floodplain forests play a pivotal role in the river ecosystem — creating wildlife habitat, improving water quality, storing carbon and slowing flooding.

But they’re disappearing.

As their name indicates, these forests generally withstand flooding, which happens on the Mississippi every year. In the last few decades, though, they’ve been swamped with high water from long-lasting floods, soaking the trees more than they can stand and causing mass die-offs. And once those taller trees die, sun-loving grasses take over the understory in thick mats that make it nearly impossible for new trees to grow.

Even before high water began to take its toll, the Upper Mississippi River floodplain had lost nearly half of its historical forest cover due to urban and agricultural land use, as well as changes to the way the water flowed after locks and dams were installed in the 1930s. A similar tale is true along the lower Mississippi.

The recent losses are worrying to scientists and land managers — especially since climate change will make extreme flooding a more frequent threat.

There’s money available to make a dent in the problem. The challenge is finding the right solution before things get much worse.

“It’s really difficult to say, ‘Why here? What caused this?’” said Andy Meier, a forester with the U.S. Army Corps of Engineers. “How do you restore it, being confident you won’t just have the same thing happen again?”

The forests on the upper river were historically made up of maple, ash and elm trees. That began to change with the onset of Dutch elm disease, first discovered in the U.S. in the 1930s. Several decades later, the emerald ash borer began to kill ash trees.

“All you’re left with is the maple,” said Bruce Henry, a forest ecologist with the Fish and Wildlife Service. “The maple gets hit with a flood, and you know, boom chicka. You’ve got a big dead forest.”

Most places on the river don’t look as bad as Reno Bottoms. There are still many trees in the floodplain, and the average person may not notice that much is wrong.

But losses can add up quickly. According to a 2022 report on ecological trends on the upper Mississippi, forest cover along the stretch of the river from Minnesota down to Clinton, Iowa had decreased by roughly 6% between 1989 and 2010. Its next segment, which bottoms out before St. Louis, had lost about 4% of forest in that time.

In some spots, those losses have escalated. Along the river between Bellevue and Clinton, Iowa, for example, forest cover dropped nearly 18% between 2010 and 2020, said Nathan De Jager, who researches the upper river’s floodplain forests for the U.S. Geological Survey.

Though it was a wet decade overall, a massive flood in 2019 caused the majority of damage, particularly in areas where the river forms the border between Wisconsin and northern Iowa, De Jager said. That flood was unusual not just for its intensity but for its duration — some trees were partly submerged for 100 days or more.

In 2020, when Reiter-Marolf was conducting a forest inventory in a stretch of floodplain near Harpers Ferry, Iowa, 35% of the trees there were dead.

It’s pretty clear that excess water is causing forest loss, De Jager said. What exactly is driving the high water isn’t as well sorted out.

But climate change, as well as changes in agricultural and urban land use, are likely factors. A warmer atmosphere holds more moisture, which can produce more intense rainfall. And that water is running off the landscape faster than it used to. One example De Jager gave is the use of drainage tiles — networks of underground pipes that suck excess water out of soil. The practice can increase crop yields for farmers, but it also sends water more quickly to the nearest river or stream. 

High water is hurting forests at both ends of the life cycle, killing adult trees as well as the seedlings struggling to grow up in the understory. And it’s triggered some other unexpected consequences, too — when the water is high, beavers can reach parts of trees they weren’t tall enough to gnaw off before.

Add to that the threats of tree diseases and invasive plants, and the distress signals are clear.

“It’s hard to pinpoint which of these stressors are the most important ones,” said Lyle Guyon, a terrestrial ecologist at the National Great Rivers Research and Education Center. “But the fact that we’ve got so many of them piled on top of each other, all happening at the same time, is certainly not helping.”

Unlike the wildfires that burn through forests and homes out west, forest loss in the Mississippi River floodplain doesn’t impact very many people’s day-to-day lives, Meier said.

But it is impacting the many creatures that call that floodplain home.

In the Lower Mississippi Alluvial Valley — the historic floodplain of the lower river — a 2020 study estimated that about 30% of today’s land cover is forest, which used to be continuous across the valley. Loretta Battaglia, director of the Center for Coastal Studies at Texas A&M University-Corpus Christi, said wildlife species loss illustrates the damage.

Battaglia, a Louisiana native who has studied forest restoration in the river valley, pointed to the ivory-billed woodpecker, a bird that once lived in the valley’s floodplain forests but is now considered by many to be extinct.

“The loss of this forest played a huge role in the extinction of that bird that needed a lot of area to fly around and do its thing,” Battaglia said.

The once-endangered Louisiana black bear faced the same hardship, she said, after deforestation fragmented the long stretches of floodplain forest it preferred to roam in.

Beyond providing habitat, trees in the floodplain also capture pollutants that would otherwise run into the river – a critical role along the Mississippi, which suffers from excess nitrogen and phosphorus that collects in the Dead Zone in the Gulf of Mexico.

The forests along the uppermost parts of the river usually don’t act as flood buffers because there isn’t much private property that abuts them, but that changes downriver in Iowa and Illinois, where big levees protect profitable farmland and towns from the river’s whims.

A study in the Journal of the American Water Resources Association found that the ability of forests to slow water played a big role in reducing levee damage on the lower Missouri River, which feeds into the Mississippi, during the river’s historic 1993 flood. More than 40% of levee failures during the flood occurred in segments of the floodplain with no “woody corridor,” as the study describes it, and nearly 75% occurred in segments where the woody corridor was less than 300 feet wide.

“The federal government could potentially save millions of dollars through management of floodplain forests,” the study’s authors wrote in their conclusion.

It’s unlikely that forest cover along the river will ever return to its original levels, Meier said. For all the usefulness it provides, though, he said “we need to do everything we can” to maintain what’s there now.

How to do that, though, can be a hard question to answer.

On a hot day in early June, Meier and fellow Army Corps foresters Sara Rother and Lewis Wiechmann planted small trees on Goose Island in La Crosse County. Mud squelched under their feet — a reminder that the river had flooded to near-record levels a month earlier — and cottonwood seeds fell from above like snowflakes.

By Meier’s estimate, none of the falling seeds would successfully grow to be adult trees. The site had too much competing vegetation, much of it reed canary grass, an aggressive species with a thick root layer that prevents trees from being able to establish in the soil.

The young trees they planted, honey locust and river birch, can handle more flooding than some other tree species. Deciding what to plant at each site is a careful calculation of how much water could pool there, how much sun it gets and which animals could potentially come through and chomp away their hard work.

Much of the time, Meier said, it’s trial and error.

A U.S. Geological Survey effort could help eliminate some of that uncertainty. Scientists have modeled flood inundation decades into the future to see which swathes of floodplain forest could thrive, and conversely, which ones will get too wet to survive.

De Jager’s team recently completed modeling for Reno Bottoms. Next year, the Army Corps and other agencies will begin a $37 million habitat restoration project to rehabilitate forests in the area.

The project, funded with federal dollars from the Upper Mississippi River Restoration program, includes close to 550 acres of forest restoration, clearing away aggressive vegetation from the understory and planting new trees. It also includes more than 50 acres where agency staff will raise the elevation of an island to give trees a fighting chance at withstanding future floods.

A little boost in elevation makes a huge difference in the floodplain, Henry said. That’s what they’re betting on.

Now seems to be a good time to do the work. Interest is growing in forest restoration, Meier said, and along with it, funding. In addition to the Reno Bottoms project, the Army Corps and the Fish and Wildlife Service have their own budgets to spend on tree planting, including millions from the Inflation Reduction Act passed last year.

The hard part, of course, is that working with trees is a long game. It could be 20, 50 or 100 years before the seedlings growing today become the mature forests of tomorrow – and in that time, the river could change, too.

It means that foresters will have to work with precision, but also with a little hope that they’re on the right track.

“You don’t really know what the result’s going to be,” Henry said. “You’re setting things in action that you’re not going to see the fruit of.”