Minnesota and Wisconsin have called a halt to commercial gillnetting in Lake Pepin after some 50 mature sturgeon and paddlefish, two of the region’s most vulnerable fish species, were found floating dead in the water near Lake City.

State wildlife authorities said the step is unprecedented but was necessary because both species are making a tentative comeback from near depletion in Minnesota waters, and many of the dead fish were mature, valuable breeding stock.

“They were really, really important animals in those populations,” said Kevin Stauffer, area fisheries supervisor for the Minnesota Department of Natural Resources (DNR). Commercial operators “are instructed that they need to avoid killing any of these fish.”

The dead fish had marks indicating they were probably trapped accidentally in gillnets along with the carp and buffalo fish that commercial operators were trying to catch.

Tim Adams, a commercial fisherman based in Wabasha, said that such incidents give the business a bad reputation, and that both sturgeon and paddlefish are relatively easy to avoid. “You never want to see that happen,” he said. “As a fisherman I’m extremely mad about this situation.”

Paddlefish, noted for their long snouts and prized caviar, are threatened in Minnesota, with only small populations known to be left in the Mississippi and St. Croix Rivers. Sturgeon, giant prehistoric fish that don’t start reproducing until they are 25 years old, are more widespread, but are still a species of special concern. Minnesota allows only a limited fishing season for them.

Both are wide-ranging fish that have been nearly wiped out by dams, overfishing, development, and pollution.

In the past several decades they have begun a slow recovery in the Mississippi and the Minnesota Rivers, a sign that water quality and habitat are improving, said DNR fish expert Neil Vanderbosch. But that also means there are more at risk of getting caught in commercial nets, he said.

“This has been a concern of ours for 30 years,” he said.

The fish kill is still under investigation, but DNR officials said it was likely an unfortunate combination of several factors. Commercial fishing boats have to avoid recreational boats, so they likely set their nets in deep water to avoid propellers and fishing lines on the surface. Sturgeon like the bottom, while paddlefish will swim through the entire water column, but may be going deeper to find cooler water. But there is less oxygen in the depths, so getting caught in deep water reduces their chances of being able to survive the experience.

Commercial gillnetters often snag one or two of the protected fish, and are required to release them and then immediately leave the area, DNR officials said. But this time of year, surface water is warm, and that makes it less likely that the fish would survive the trauma.

“You have to have better judgment when you are netting,” said Adams.

Stauffer said several operators probably contributed to the kill, and the wind pushed the carcasses into one area. A total of six operators are licensed to catch rough fish with either gillnets or seines, and they’ve been busy on Lake Pepin this summer. Prices for carp and buffalo fish are high, and summer aquatic plant growth is keeping them out of other areas on the rivers, Stauffer said.

Commercial gillnetting will be suspended until at least September, officials said. Then cooler water temperatures will make it more likely that the fish can recover if they are caught in nets, and there will be fewer sports fishing boats on the water. Seine netting will still be allowed, because they corral fish inside a net instead of trapping them in webbing, and the fish are not harmed when they get tossed outside the net. But using seine nets requires more labor and is more expensive.

Or commercial operators can go elsewhere on the rivers to use gillnets.

In the meantime, DNR officials and commercial fishing operators will try to come up with other solutions for Lake Pepin. That could include banning gillnetting during the months when Lake Pepin is busy and the fish are vulnerable, said Adams.

“Outside these few hot months, everything is fine and dandy,” he said.