Next week will likely mark the end of the Confederated Salish and Kootenai Tribes’ spring gill-netting season, part of the tribes’ effort to boost the Flathead Lake’s threatened bull trout population by suppressing non-native lake trout.

Barry Hansen, fisheries biologist at the tribes’ netting facility in Blue Bay, explained that the program kicked off last year in an attempt to augment the removal of lake trout through the Mack Days fishing contests each spring and fall, which together reel in about 50,000 lake trout per year.

“We’re growing the contest over time, and continued to monitor and didn’t see that we had removed enough,” Hansen said. “How big can we get these contests? Probably not big enough, that’s why we started with the netting.”

Lake trout suppression has been used as a recovery tool for native fisheries in other lakes. Like many other bodies of water in the Northwest, Flathead Lake for decades supported several relatively stable sport fisheries, including native bull and cutthroat trout, along with introduced lake trout and kokanee salmon.

However, upstream introductions of mysis shrimp led to the invasive species finding its way down into the lake. The shrimp population exploded, and with it the population of lake trout.

Lake trout feeding habits are more in sync with those of the shrimp, allowing the lake trout to reap the benefits of the new prey, grow larger and displace native species through competition and predation. Kokanee salmon disappeared entirely, with an estimated fishery of 300,000 salmon dropping to zero in the span of five years.

For the tribes, though, the main issue was the loss of native fish, on which their ancestors had relied.

Bull trout are now listed as threatened under the federal Endangered Species Act, and Hansen oversees an aggressive program aimed at recovering the species.

“It’s very important for [the tribes] to see those numbers built back up,” Hansen said. “Also, cutthroat trout are not listed under the Endangered Species Act, but they’re important to them.”

The tribes’ program is still evolving as tribal biologists experiment with different mesh sizes, locations and timing to get the most bang for their buck.

After predicting the netting program would remove about 30,000 lake trout last year, the 2014 spring and fall netting seasons were relatively underwhelming, bringing in just 7,700.

In their environmental study, the tribes set a goal of reducing the lake trout population by 75 percent over 50 years through general angling, the Mack Days tournaments and gill netting. That alternative calls for removing 143,000 lake trout each year.

This year’s numbers are up, however, with about 10,000 fish caught in less than three months on top of 32,179 brought in during the spring installment of Mack Days.

The fish are processed at the Blue Bay facility, where a new $62,000 filleting machine quickly readies the meat to be shipped to food banks from Whitefish to Missoula.

Hansen said crews have been dragging nets with a four-inch mesh (targeting fish at least 22 inches long) close to shore, where lake trout gather to spawn. By keeping the depth at about 250 feet, netting crews can generally avoid accidentally snagging other fish — or by-catch — and Hansen said bull trout venturing that deep are generally small enough to evade capture.

“We’ve had more time to learn how to target netting better, we’ve had better whitefish by-catch, and no bull trout by-catch this year,” he said, adding that last year resulted in only one bull trout mortality.

The issue of by-catch was a major sticking point a few years ago, creating a rift between the tribes and Montana Fish, Wildlife and Parks. The state agency co-manages Flathead Lake with the tribes, whose reservation spans the southern half of the lake.

Last year, the U.S. Fish and Wildlife Service approved the tribes’ gill-netting plan, granting them a three-year permit to begin operations.

The state wildlife agency initially had worked with the tribes to develop the netting program but pulled out in 2012, objecting that the scope of the project had changed dramatically from the 2010 proposal and that public involvement was inadequate.

State officials also questioned estimates of bull trout by-catch, stating in a 2013 position paper that “if there is a there is a high level of by-catch of bull trout in gill nets, then gill netting could offset the possible gains and hurt the bull trout population.”

Other concerns expressed by the agency included potential damage to the local food web, as well as impacts to recreational fishing.

“The last co-management plan expired five years ago, and the tribes and the department have different interpretations of parts of that plan,” said Mark Deleray, the regional fisheries manager for Fish, Wildlife and Parks. “We weren’t comfortable that the co-management plan was directing us to do that kind of activity.”

However, he stressed that the state and tribes work closely together on a wide range of other issues, including monitoring fisheries, water quality and habitat protection, public education and other fisheries management strategies, including the Mack Days tournaments.

The most recent 10-year co-management plan was adopted in 2000 after 16 months of work by state and tribal officials and citizen advisory groups. It expired in 2010 and Deleray said there isn’t currently any dialogue between the two parties talks to draft a new one.

“I think we’re going to learn from what the tribes are doing, and we’re going to continue to work with them very closely on those aspects where we currently are working with them,” he said.

More active in their objections to the suppression efforts are many of the guides on the lake who make their living taking visitors to the valley out on fishing trips.

Mike Jousma is the new owner of Captain Norm’s Fish-N-Fun, a Lakeside charter boat company.

He said the tribes have ignored the concerns of outfitters that depend on a healthy sport fishery, and that the quality of lake trout fishing has dropped dramatically since their suppression efforts began.

“We as guides are concerned that as soon as lake trout are down to the point that it’s not even a fishery, what’s there going to be to fish for?” he said.

“Ten years ago you could throw anything in there and you have 20, 30-fish days. Now you’re constantly changing tactics and you’re lucky if you get five. You could at least guarantee that people would get their money back if you didn’t catch fish, but you can’t even claim that any more.”

He also echoed a concern voiced by the state when it pulled out of the netting plan: If lake trout populations go down, mysis shrimp populations could increase substantially. The shrimp consume zooplankton, which in turn keep algae in check. A jump in the mysis shrimp population could potentially bring down zooplankton levels, which could in turn result in more algae in the lake.

“In my mind, you’re going to lose one of the things that people come to Flathead Lake for, and that’s the beautiful, pristine waters,” Jousma said.

Tom Bansak, a research scientist at the University of Montana’s Flathead Lake Biological Station in Yellow Bay, said that’s exactly what happened when the shrimp originally landed in the lake.

“Really, mysis shrimp was a significant event,” Bansak said. “The arrival of mysis shrimp feeding on the zoolankton, feeding on the algae, caused Flathead Lake to become about 30 percent greener.”

He said current algae levels since that event are “tenuously stable,” but acknowledged limitations in biologists’ understanding of the lake ecology. For the last 2 1/2 years, scientists at the facility have been working to develop a model that can predict the effects of changing conditions in the lake, from lake trout removal to different levels of nutrients entering the lake from rivers and streams.

“You can plug in different populations of lake trout and see how that affects other areas of the lake,” he said. “You tweak different aspects of the community in the model to see what effects and what results occur elsewhere in the ecosystem.”

Until their permit expires in 2017, the tribes will push forward with their netting efforts.

Whether the combined suppression tactics pay off for native fish populations is still an open question, but Bansak said a return to the Flathead Lake of yesteryear is unlikely anytime soon.

“The arrival of mysis shrimp changed Flathead Lake dramatically,” he said. “You have one lake before mysis shrimp, and you have another lake after mysis shrimp.”

Reporter Samuel Wilson can be reached at 758-4407 or by email at swilson@dailyinterlake.com.