Lake Mille Lacs resort owners are angry, anglers are frustrated, and they all have an opinion on what’s to blame for the shocking decline in walleye in Minnesota’s favorite fishing destination.

But there’s one culprit that gets scant attention: global warming.

Tullibee, a cold-water loving fish that is a critical prey for walleye, is largely gone from Mille Lacs. In fact, tullibee is in trouble across the state — a clear sign that Minnesota’s lakes are changing as fast as the climate and creating an uncertain future for the state’s prized fishing industry.

By the end of this century, tullibee will be gone or drastically reduced in two-thirds of the lakes where it lives now, according to a sophisticated climate prediction model by state and University of Minnesota scientists. Other coldwater fish like yellow perch, burbot and lake trout are also declining, while warmwater fish like bluegill and crappies are on the rise.

“It’s a pretty striking story,” said Peter Jacobson, a fish biologist with the state Department of Natural Resources. He’s been studying tullibee since heat-related fish kills first got his attention in the hot summer of 2006. “The recent declines have been mostly from climate.”

The shift is dramatic enough to inspire an unusual effort to create refuges for the vulnerable fish species by permanently protecting some of Minnesota’s cleanest, coldest lakes that are scattered like jewels across the northern forest. Before it’s too late.

“It’s such a daunting issue,” Jacobson said.

In Mille Lacs, there’s a lot more going on in the predatory life of fish than just climate change. Young walleye are getting eaten before they grow up by a rising population of northern pike and cannibalistic larger walleye. Thanks to invasive zebra mussels and laws that shut down leaky septic systems and animal feedlots, the water is cleaner and clearer, making the little walleye easier to see. The population of smallmouth bass, a fish happy in warmer waters, has exploded in recent years — but walleye don’t eat them. Meanwhile, tullibee and the yellow perch that walleye do relish are disappearing, and other well established invasives like spiny water flea and milfoil are changing the ecosystem in unpredictable ways.

Resort owners pay price

This year, the DNR set a walleye harvest target for the lake at 40,000 pounds — a third less than last year and down a stunning 84 percent from 2013. That, they hope, will help give the walleye a chance to recover.

For now, Mille Lacs resort owners will pay the price.

“For the first time in years I am not sold out at the opener,” said Linda Eno, who, with her husband, owns the Twin Pines resort. She blames the DNR for years of mismanagement and overnetting by Indian tribes, long a sore point with resort owners.

“You cannot blame spiny water flea, zebra mussels and global warming,” she said. “That drastic of a change does not come from those minor things.”

But fish biologists and climate scientists say that global warming’s impact on Minnesota’s lakes is anything but minor.

State wildlife managers first became alarmed in 2006, when they noted tullibee kills in 18 lakes during temperature spikes in July, Jacobson said. That’s when they decided to launch a long-term project to use tullibee, also known as cisco and lake herring, as a barometer for climate change.

“Cisco is the most tolerant cold water fish species,” said Heinz Stefan, an engineer at the University of Minnesota’s St. Anthony Falls Laboratory, who led the design of the lake climate change model. “They can handle higher temps and are a very important as a food source for predator fish like pike and walleye.”

In other words, if they can’t survive, then other fish won’t either. But they won’t be alone. A major study published last week in the journal Science found that if greenhouse gases and average temperatures continue to rise at current rates, the world will see a major loss in diversity. One in six species around the globe could disappear because they can’t move or adapt fast enough to changing habitat.

Two-thirds of lakes at risk

In the 620 Minnesota lakes that are home to tullibee, it plays out like this. In deeper lakes, the water stratifies into layers of increasingly cold temperatures. When a lake gets hot at the surface, the tullibee go deeper. But they also need good supplies of oxygen, which can be scarce at the bottom. So they try to find that sweet spot that is cold enough and has enough oxygen.

Using decades of weather data on Minnesota’s tullibee lakes, plus sophisticated predictions of how rising average temperatures will affect ice-out, lake mixing and plant growth, researchers came up with a prediction: By the mid to late part of this century, two-thirds of those lakes will be inhospitable for tullibee. And not just because they are heating up.

Longer summers result in less mixing of lake water layers, which means less oxygen makes it to the bottom. The tullibee, Stefan said, “get squeezed upward by low oxygen and then they encounter warm temperatures.”

It’s not just the gradual warming — it’s also the sudden hot summer spikes, especially in shallower lakes like Mille Lacs. “With a really serious bounce in temperature you’ll see fish rolling over pretty good,” said Eric Jensen, a Lake Mille Lacs specialist for the DNR.

This doesn’t mean walleye will disappear. They are doing fine, if only because the DNR stocks them in 500 to 600 lakes where they don’t always reproduce naturally.

But in the lakes they share with tullibee, walleye will likely be smaller, Jacobson said. “We are not going to lose walleye because we are losing [tullibee],” Jacobson said, “We are just going to lose trophy walleye.”

Now the DNR is starting to see declines in other cold water fish such as lake trout as well.

Meanwhile, warm water largemouth bass are suddenly appearing in lakes around Duluth where they’ve never been seen before, said Bethany Bethke, a DNR fish biologist who’s studying long-term trends in Minnesota fish.

‘Refuge lakes’

The tullibee climate prediction includes a more optimistic scenario as well. Minnesota has lakes where cold water fish may be able to survive the global heat wave that’s coming — 176 that are already considered state treasures. They are all deep, exceptionally clean, and primarily in the north — and they’ve already proven their value. When tullibee floated belly up in other lakes after recent heat waves, they had no problem riding out the heat in these cold northern lakes.

The state has launched an ambitious plan to make all of them “refuge lakes” for cold water fish like tullibee. Most hug the border with Canada and are protected by the Boundary Waters Canoe Area Wilderness. Thirty-eight lie in four counties around Leech Lake in north-central Minnesota, including popular cabin lakes such as Roosevelt and Ten Mile. If 75 percent of the watershed around each refuge lake can remain in forest or in its natural state, that should keep the lakes sufficiently clean and well-oxygenated at their depths to preserve cold water species, Jacobson said.

But that will cost money. The DNR has received about $6 million from the state’s Legacy Clean Water Fund to pay property owners around some of those lakes to keep their land undisturbed through permanent conservation easements and outright purchases. But the project will require much more in future decades — about $180 million — and for now there are more willing property owners than money.

Candace Gouze and her husband have been slowly buying up land around their lake home on Roosevelt Lake, and now own 160 acres. They hope to put easements on some of the land to protect the lake and the loons that nest nearby along the shore, even though it reduces the dollar value of the land.

“I have this feeling that if we all do something, then we can affect climate change,” Gouze said. “To not do anything is not an answer.”