Fishing for science: Researchers cast nets in the newly-freed Klamath River

Under a lead-gray sky on a cold, rainy November morning, James Whelan follows a small procession of trucks on a bumpy, rutted-out road along the Klamath River in northern California. Driving a stick shift while wearing a wetsuit is tricky, but nothing compared to the tangle-net survey he’s about to lead.

“This is definitely the most unique type of netting I’ve done,” says Whelan, project manager for California Trout. “Alright, just go jump in the river and hold onto the other end. By the way it’s pretty sketchy…yep, I figured that out pretty quick!”

Whelan and a small crew are sampling at four different locations along the Klamath River at and upstream of the old Iron Gate dam site as part of the Klamath River Monitoring Program. They hope to catch and tag any large fish that are in the river right now—Chinook salmon, steelhead, and possibly, coho.

The tangle-net surveys are part of the comprehensive monitoring that’s happening since four dams were completely removed from the Klamath River earlier this year. Agencies, tribes, conservation organizations, and researchers are eager to follow fish as they explore the reconnected habitat above the dams.

“The major questions we’re answering are really foundational,” says Damon Goodman, Mount Shasta-Klamath regional director at California Trout. “How many fish are entering their historical habitats? What species, and where do they go?”

Actually answering these questions requires many hands. On this day alone, Whelan’s crew includes technicians and biologists from Oregon Department of Fish and Wildlife, California Department of Fish and Wildlife, the Karuk Tribe, and the Bureau of Reclamation.

The first site is at the top of Ward’s Canyon, just below the old Copco 2 powerhouse. Whelan and Alex Corum, fisheries biologists with the Karuk Tribe, wade into the river with the net while five of their crew wait in the shallows with an assortment of buckets and nets. Soon, only Whelan’s head bobs above the water as the swift current carries him. Once he’s downstream of Corum, he swims to shore, and the crew fans out along the outstretched net.

Whelan says you can usually feel it when a fish hits the net.

“You’re never quite sure at first, but if you start feeling them roll and shake and tangle themselves up you’re like, oh yep, that’s a fish…sweet!”

But this time, they’ve caught nothing but driftwood.

Complementary tools

After the dams were completely removed this fall, Chinook salmon began exploring the new territory almost immediately. Fish biologists scrambled to get personnel and protocols in place.

“As soon as we had our gear together, the fish showed up, so we’ve been running to keep up with it ever since,” says Corum.

He and Whelan began tangle-netting in September. They are tagging every large fish they catch in the nets with a passive integrated transponder, or PIT tag, and radio tags. Thanks to mobile trackers and a series of 15 stationary receivers, they can track any radio-tagged fish from the old Iron Gate dam site all the way to Upper Klamath Lake in Oregon.

The collaborative has also installed a sonar station in the river at the Iron Gate dam site. The device uses high-frequency sound waves to create “movie-like” images of any fish that pass by it.

“Sonar is being used at this location as a counting station to get an understanding of how many fish are running into this new habitat above the former Iron Gate dam,” says Corum.

The sonar is very precise, and it can “see” fish no matter how murky the water is. On one day in October, it detected 290 fish that measured over 20 inches. Most of these were likely Chinook.

Keith Denton, a sonar consultant from Washington State, says the technology was first developed to detect mini-submarines. Denton has been using sonar to track fish on the Elwha River in Washington State for 15 years. Since two dams were removed from that river in 2011 and 2014, steelhead, Chinook, and coho runs have been expanding into habitat that was previously inaccessible.

“The sonar imagery is perfect. Not only do you get the total number, you also get run timing,” says Denton. “This is information that literally didn’t exist before that we now have access to.”

Denton is consulting with partners on the Klamath on the sonar technology and data analysis; he’s also helping crews tweak their netting technique.

Learning to read the river and select the best spot for deploying the net takes time, says Denton. “It can be kind of intimidating; you’re dragging around this 20-meter net in the river, you’ve got dry suits on, the weather gets crappy…but to be honest with you it’s my favorite part of the job.”

One thing the sonar can’t do is accurately identify species. For example, while adult Chinook are hard to mistake for anything else, young males, called jacks, can be about the same size as a large steelhead.

The tangle-net surveys help validate what the sonar eye sees, says Whelan.

“That’s another reason we’re doing these netting surveys is trying to catch fish and almost proportion out: How many Chinook are there versus how many steelhead are there? How many jacks are there versus how many adults are there?”

They will continue netting through early spring, but the sonar station will stay in the river most of the year.

“We’re pushing this monitoring to be as holistic as possible,” says Goodman. “We’re going to learn things about all kinds of different fish, which are all important to the ecosystem.”

One fish at a time

The second of two sites Whelan’s crew samples is a place on the river called Copco Village. It’s near Fall Creek, where the hatchery has been relocated.

The technicians note a deep, quiet pool on the far side of the bank that looks “fishy,” and right away someone spots a large male Chinook salmon near a gravel nest, or redd.

“That’s a big one,” says Whelan. “That’s a big fish if we could figure out a way to get him.”

They decide to deploy the net slightly upstream so they don’t disturb the redd. On their second pass, they net a large female steelhead.

Jacob Peterson, a fish technician with ODFW, carefully untangles the fish and uses a small dip net to guide it toward the bank, where a floating trap is waiting.

“She’s starting to ‘chrome out;’ I think she’s an actual downstream steelie,” says Corum.

The fish has a rosy blush down her side, but the rest of her body is silvery—a sign that she’s come up from the ocean to spawn. Unlike salmon, which die after they return to freshwater, steelhead can spawn multiple times. Those that stay in freshwater their whole lives are called rainbow trout, and the prized rainbows in the Upper Klamath Basin are known as redband trout.

Corum, Whelan and Carolyn Malecha, a fish biologist with ODFW, squat next to the fish, while the rest of the crew huddles around them.

“We’re going to need scissors for genetics, and the envelope for info,” says Malecha. Quiet descends as she measures the fish and clips a sample from the dorsal fin—this will yield information about the genetic markers related to run timing.

Next Malecha fits the steelhead with a tiny passive integrated transponder, or PIT tag, and a much larger radio tag. This device is about the size of a roll of nickels, and each one costs about $200. It will “ping” every six seconds or so, allowing for precise tracking.

Five minutes later, the steelhead is swimming freely again.

They take another pass with the net, hoping to catch the Chinook, but it eludes them. After a full day of sampling, they only catch and tag the one steelhead.

Since they began sampling in September, the partners have tagged four fish—two Chinook and two steelhead. Thanks to the telemetry stations and mobile trackers ODFW staff have been deploying via truck, they’ve tracked one of the Chinook across the Oregon border. But even as the fall Chinook season winds down, they’re looking ahead to the coho run, which should start any day now.

Goodman of Cal Trout says it’s important to remember this is a long-term project. The sampling effort will continue for at least five years, not only adding to the body of knowledge on this dam removal project, but others yet to come.

Similarly, it will take several generations of fish to rebuild the number and diversity of fish throughout the Klamath watershed.

“The Elwha helped us understand this, and it’s a much smaller drainage area,” says Goodman. “We’re at the beginning of this story, not the end.”

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