Auke Lake: home to Southeast standbys, uncommon species

Auke Lake may be the first place many Juneauites think of for fresh water recreation, but it’s also a unique ecosystem with more to it than is immediately apparent.


Fresh water mussels (uncommon in Southeast Alaska), a rare dragon fly, a small population of steelhead trout — all make their homes at Auke Lake. So do all species of salmon except Chinook, as well as stickleback and sculpin.

The watershed is also an important over-wintering site for dolly varden char and cutthroat trout, and it’s unique in that every single fish and fry — every single one — is counted leaving or arriving in the lake by the National Oceanic and Atmospheric Administration’s Auke Creek Research Station. Because of this vast amount of detailed data, the creek has spawned a large number of theses and dissertations, and it’s an important indicator station for the health of salmon stocks across Southeast.



The Auke Creek Research Station is manned primarily by manager John Joyce, a Fishery Research Biologist with NOAA, and Scott Vulstek, a fishery biologist working on contract for NOAA. At times, the two (sometimes assisted by graduate students or Alaska Department of Fish and Game employees) count more than 200,000 fry, smolt, char and trout leaving the lake in the spring. They also count thousands of fish returning in the fall.

The station is the only place anywhere, as far as Joyce and Vulstek know, counting pink salmon fry.

They also take samples and conduct experiments.

Right now, Joyce and Vulstek are incubating about 50,000 sockeye eggs (now hatching) to assess the long-term fitness of populations with both hatchery and wild fish.

“There’s a lot of (fishery and fish population) enhancement in Alaska, and it’s really done very well … but it’s always good to keep a check on what potential impacts you could have,” Joyce said.

The study has been going just a few years, but they hope to get it funded for the life cycles of at least a few generations of fish — between 12 and 24 years.

“This place is all about long-term, and it’s hard to get long-term funding,” Joyce said.

University of Alaska Southeast Associate Professor of Biology and Department Chair David Tallmon also emphasized the importance of the station.

“Auke Creek is an amazing resource because it’s a complete census of all the fish going out and going in every year,” he said. “It’s a pretty heroic bit of work.”



“We know what comes and goes, but we don’t necessarily know what’s in the lake, because they don’t have a regular pattern,” Joyce said of the fish.

Coho, sockeye and kings spend at least a year in the water. Sockeye and coho spend the winter in the lake — sometimes two. Dolly varden and cutthroat trout stay in the lake, then leave and spawn in nearby creeks.

The only way to figure out whether or not the station counts the same fish more than once — leaving in the spring and returning in the fall, for example — is with individual tracking.

ADF&G Coordinator for Fish Habitat Partnerships Roger Harding said between 1999 and 2005, the department found that about 250 to 675 coastal cutthroat larger than seven inches lived in Auke Lake.

Mature cutthroat were tracked in the mid-90s and found to range at least from Hilda Creek (on the back side of Douglas) to Cowee Creek. Radio telemetry studies found cutthroat heading into Montana Creek, Mendenhall Lake, North Douglas’ Peterson Creek and others.

About five years earlier, dolly varden were tagged leaving Auke Lake and caught by fishermen “all over the Juneau road system.”

More recently, the U.S. Fish and Wildlife service conducted a study on sockeye spawning around Auke Lake.

Neil Sticher, a habitat restoration biologist at the U.S. Fish and Wildlife Service, said a 2012 study funded by ADF&G’s Alaska Sustainable Salmon Fund and conducted by former Fish and Wildlife Service biologist James Ray shows the importance of Auke Lake’s tributaries — Lake Creek and Lake Two Creek, specifically.

Ray tagged 80 sockeye arriving at the weir. Of those, 86.8 percent spawned in Lake Creek. In Lake Two Creek, 8.8 percent spawned. In other creeks, 2.9 percent spawned. The final 1.5 percent spawned in the lake itself.

“The long-term sustainability of the population relies on very prudent management of both Lake Creek and Lake Two Creek,” Stichert said.



Using data provided by the research station, Tallmon and the lead researcher in a recent study, then-University of Alaska Fairbanks PhD student Ryan Kovach, found climate change causing “some pretty dramatic shifts” in the run timing of a number of species of fish in Auke Creek.

The run times of coho and pink salmon, both on even and odd years, as well as sockeye, dolly varden char and cutthroat trout have become compressed. Pinks have undergone some evolutionary changes, losing a marker that indicates an early run.

On a positive note, while climate change is affecting the fish’s run timings, their populations are stable long-term.

“Abundances seem to be fairly resilient and robust,” Tallmon said.

He said they don’t know how much the Auke Creek changes indicate changes in other systems. Southeast Alaska has a large amount of variation in streams, and Auke Lake is different from, for example, Mendenhall Lake in that it doesn’t have any glacial influence, he said.



Auke Lake is also home to freshwater mussels.

“There are not many freshwater mussels in Southeast Alaska,” said Fish and Wildlife Service biologist John Hudson. “It’s really neat to see ... They’re usually lying down in the rocks and on the bottom and filtering away.”

Tallmon said not much work has been done on Auke Lake’s freshwater mussels, but “it’s probably a genetically very divergent population.”

A few years ago, Hudson found a new species of dragonfly for Alaska — the Ocellated Emerald — in the Arctic. A few months later, he was collecting at the outlet of Auke Lake and found some there.

“I was just floored,” he said. “It was just so neat to see a new species. It’s kind of neat that Auke Lake is a special enough place to harbor that species … it surprised me, since I’d spent so much time looking in Juneau.”



Almost the entire resident population of the Mendenhall Wetlands State Game Refuge’s Vancouver Canada geese take refuge in Auke Lake during hunting season, said local naturalist and author Bob Armstrong. Generally speaking, that’s between 500 to 700 geese.

“When hunting season begins, that’s where they escape,” he said. “It appears that it’s almost the entire population.”

About 10 years ago, he and others did surveys documenting the birds’ movements.

During the non-breeding season, they live on the Mendenhall wetlands. They also fly over Admiralty Island for nesting, and go to Glacier Bay during molting season.

And now, they go to Auke Lake, as well.

The birds leave in the morning, either when the first gun is fired or before, spend the day at Auke Lake, and then fly back to the wetlands at night and feed, he said. Mallards have learned to do the same thing — Armstrong said he’s counted up to 1,000 ducks in a day on the lake.

Armstrong said the lake is freezing over later than it used to, which is also a factor in the daily migration.



“In general, Auke Lake is a pretty healthy place,” Joyce said.

It’s not immune to human interference, however: In the recently published ‘A Natural History of Juneau Trails: A Watershed Approach,’ author Richard Carstensen lists several changes to the lake’s species.

“Longtime residents and researchers report that Auke Lake is in surprising flux for a hydrologically stable, bedrock-controlled lake surrounded by old-growth forest,” he wrote.

Shore nesting waterbirds, like the common loon, are declining, for example. The western toad is “functionally extinct.” And the freshwater mussel population is declining, which “may be related to hydrocarbons from increased motorized recreation,” he said, citing a 2008 study.

The Juneau Watershed Partnership also has quite a bit of comprehensive information about the overall health of the lake. A 2009 assessment from the group points to declines in salmon populations and emphasizes the importance of good management.

“(The lake) is a great resource for the community for recreation, but also for fish studies — and it’s right in our backyard,” Tallmon said.


• Contact Outdoors reporter Mary Catharine Martin at



Juneau Empire photographer Michael Penn created this presentation on Hudson’s search for dragonflies.
More information about Auke Lake fish


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Sport fish report for May 14, 2018

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