San Joaquin River salmon make big gains, but don’t call it a comeback yet
November 22, 2018
Fresno Bee by Lewis Greenwold
Fish biologists bringing back salmon runs on the San Joaquin River say a record number of fish nests have been found in the river below Friant Dam east of Fresno.
The number of nests, called redds, created by spring-run Chinook salmon reached 41 this year, compared to just 13 last year.
“It’s a vast improvement over previous years,” said fish biologist Don Portz, manager of the San Joaquin River Restoration Program. “That’s triple the amount.”
The numbers are encouraging to fish scientists because they show the restoration program is making progress in re-establishing a wild salmon fishery on the San Joaquin after six decades of absence. But there’s a lot of work to do before scientists can say they’ve done all they can.
“Right now we’re in the infancy stages of bringing the fish back,” Portz said.
Last year, for the first time in 60 years, spring-run Chinook salmon successfully reproduced in the river, which made headlines.
To monitor the fish after they hatch, biologists are installing special nets, called emergence traps, directly on top of nine redds. The nets are designed to catch, but not kill, emerging salmon fry.
So far this year, no salmon fry have been found, but it’s early yet. It takes a couple of weeks for fish to hatch and a lot depends on water temperature. But when they appear, experts will count them, weigh them, measure them and test for genetics.
“I think it’s incredibly rewarding work to see how the fish are actually thriving in the sections of the river we are working on,” said fish biologist Stephanie Durkacz, who donned waders and installed several traps over the past two weeks. “There haven’t been spring-run chinook salmon spawning here in 60 years. ... It feels very historic.”
Turning the ‘spigot’ back on
The work is being done because an agreement with environmentalists requires the federal government to restore the lost salmon runs. A long stretch of the San Joaquin River dried up and with it the salmon when Friant Dam was built in the 1940s.
Several fish biologists, lawyers and members of the public recently toured the river with the Water Education Foundation, based in Sacramento. Portz, the river restoration program manager for the Bureau of Reclamation, laid out the stakes.
“This is a river that didn’t have flows for over half a century,” Portz said. “It’s not an easy thing to turn on the spigot and let water start flowing again.”
But hatchery-raised adult salmon released into the San Joaquin River are making redds and spawning, giving fish scientists hope for success.
A major goal of the restoration program is for salmon eggs laid naturally in the river to hatch and for juvenile salmon to swim to the ocean, reach sexual maturity, then return as adult salmon to spawn and die — and for the cycle to start all over again as it did for time immemorial.
That’s how it was until Friant Dam blocked the river in 1948 and the water stored in Millerton Lake was diverted to farms on the Valley’s east side as part of the federal Central Valley Project.
But under California fish and game code, dams must release enough water to keep fish alive downstream.
In 1988, the Natural Resources Defense Council sued the U.S. Bureau of Reclamation, which controls the dam, and all of the irrigation districts that use the water for farming. A federal judge sided with the NRDC.
At the judge’s urging, the parties in 2006 hammered out the San Joaquin River settlement mandating that both spring and fall salmon runs be restored, from Friant Dam to the confluence of the Merced River a distance of 153 miles.
Seeking a self-sustaining salmon population
There are two kinds of salmon in the San Joaquin River — fall run and spring run salmon.
Spring run salmon evolved to take advantage of spring pulses of snowmelt rushing down from the Sierra Nevada. Historically, the fish swam up from the ocean and lived in deep pools of cool water during the summer, then spawned in the fall.
By contrast, fall run salmon arrived in late November to early December and quickly spawned. Both spring run and fall run juveniles swim to the ocean in the late winter and spring.
“If you can’t bring them both back, we’re supposed to focus on the spring run,” Portz said.
The fish that hatched in the river late last year are spring run salmon. It was considered a major milestone.
The work has been slow to ramp up, but Portz says they’ll have all the necessary work completed by the end of 2024 so both spring and fall run salmon can swim unimpeded from the ocean to Friant Dam.
The Natural Resources Defense Council is keeping a close watch on developments.
“Progress is slower than required, and that is disappointing,” said NRDC lawyer Doug Obegi in an interview with The Bee. Still, he said, “we should have a fully functioning river, and that’s encouraging ”
The effort is funded by state and federal governments. Eastside farmers pay a “Friant surcharge” for their irrigation water, and the collected funds, about $8 million a year on average, is paid to the federal government.
Portz said the original cost estimate for the restoration work was $1.5 billion to $1.6 billion, but program managers gave the budget a “haircut” to cut costs. “It still came to $648 million for just phase one,” he said.
Costs include a new fish hatchery near Friant Dam, which is behind schedule but should open next year. The hatchery will eventually produce 1 million salmon fingerlings annually. An interim hatchery on the river now produces 200,000 fish per year.
The hatchery is needed because naturally producing salmon on the river won’t be enough to restore the salmon runs, at least at first.
“We want a naturally reproducing, self-sustaining population, but you need a supplement,” Portz said.
What’s the next milestone?
So far, returning adult Chinook salmon have not yet been seen in the San Joaquin River. But Portz and the other scientists have their fingers crossed that salmon will start showing up on the San Joaquin next spring.
When that happens, “the returning adult spring run salmon will be the next milestone for the program,” he said.
Because of physical barriers still in the river that stop the migrating fish, the fish will be netted downstream and trucked to the waters below Friant Dam, he said.
There currently isn’t enough water in the river to support a fully functioning salmon fishery, Portz said. Levees will be built where needed so the channel can contain more water, he said.
There’s also a need to build “fish passages,” man-made structures allowing fish to swim around dams and get upriver on their own, which biologists call “volitional passage.” The fish passages will be built by 2024 as required by the settlement, Portz said.
But it’s water temperature that is the crucial factor for salmon survival, he said, especially for juvenile fish going out to the ocean. That’s why cool water at the bottom of Millerton Lake must be sent downriver.
“We have to time our releases effectively,” Portz said. “We need to have planned pulses to move the juvenile fish and start their migration to the ocean.”
The settlement requires water in the river all year long. That leaves less irrigation water for farmers — about 15 percent to 20 percent less per year on average than before the settlement.
But the farmers are banking on there being no more reductions and support bringing back salmon on the river.
“Friant Water Authority continues to be invested in the long-term success of the San Joaquin River Restoration Settlement and program,” the water delivery agency said in a statement. “We believe the terms of the settlement were fair and we’re working with our partners to fully implement it.”
One major unknown, meanwhile, is the effect of climate change on the San Joaquin River salmon. Spring run salmon would probably do better than fall run salmon in an era of global warming, Portz said.
“Because they spawn earlier in the fall, they move out earlier in the year: February, March, into April,” he said. “Water temperatures are still cool.”
But it means managers must make the right calls so the adult salmon will return despite climate change, he said.
“People are going to say, ‘This can’t be done,’ ” Portz said. “But if we do our fish passage right, and provide the habitat that’s necessary, I think it is attainable.”
Other work includes creating rearing habitat for salmon, adding screens to keep fish from migrating into side channels where they would get stranded, and building a fish screen, to be the largest in the state, to keep salmon out of Mendota Pool on the Valley floor.
Additionally, more gravel must be put in the river so returning adult fish can create their redds.
Butte County Town Attempts to Save Salmon From Wildfire Devastation
November 21, 2018
KQED by Chloe Veltman
Despite being evacuated nearly two weeks ago from their homes in the wake of spreading wildfires, residents of the town of Butte Creek Canyon — a few miles east of Chico — plan to join forces Wednesday to save the local salmon population.
Locals are very proud of these fish.
"Butte Creek spring-run salmon are one of the only remaining populations of wild spring-run salmon left in California," says Allen Harthorn, executive director of The Friends of Butte Creek, an organization that works to protect the fish, which were once near extinction.
Now, the fish face a new danger, as rains threaten to wash toxic debris from the nearby wildfires into the creek.
"The ash and toxic components in the runoff could just saturate the creek, fill it up with sediment and wipe out this entire year class of spring-run salmon," said Harthorn, who spoke from a friend's home in Chico 12 days into his evacuation from Butte Creek Canyon. He said around 100 homes had been destroyed in his town, though his house escaped the flames.
With the spawning season recently over, the problem is particularly acute for newborn fish.
The juvenile salmon at this point are at a very critical stage," said Harthorn. "The adult fish finish spawning about the middle of October. So all of those eggs were in the gravel. They've probably started emerging from the gravel in the last week or so, out swimming around in the creek."
Following a callout on The Friends of the Butte Creek's Facebook page, Harthorn said around 50 volunteers planned to spend Wednesday laying down 800 long rolls of straw, called "wattles," near burned-out residences and streams.
The hope is to ease the flow of the creek and capture the debris.
"The straw wattles will slow down the movement of the water and allow it to seep in as well as capture the ash and potentially other toxic components," Harthorn said.
The task ahead is huge. And Harthorn is also worried about the run-off flowing in from other nearby places destroyed by fire, particularly Paradise.
"The unfortunate thing is that Butte Creek meets up with all the tributaries that come off Paradise out in the valley," Harthorn said. "And all those tributaries are going to be carrying all the runoff from Paradise, which has 5 to 10 times the volume of material and destruction that the Canyon had. So it's going to be a lot worse. There is a huge effort out there to protect the water quality. But it's going to be a massive job."
Another big year for salmon on Mokelumne River
November 20, 2018
Stockton Record By Dan Bacher / Record Correspondent
The Mokelumne River Hatchery in Clements is once again seeing big numbers of fall-run Chinook salmon returning from the ocean this autumn. The run is 1,617 fish behind the numbers seen last year at this time, but this run is still going to be one of the top three recorded on the river.
The count over Woodbridge Dam on the Mokelumne to date is 13,467 salmon, including 8,779 adults, reported William Smith, California Department of Fish and Wildlife (CDFW) hatchery manager. That compares to 15,086 fall chinooks by the same time last season.
A record number of fall-run Chinook salmon, 19,904, went over Woodbridge Dam in the fall of 2017. Early dam counts indicated an increase over last year’s run, but the numbers since then have fallen behind those of last year.
More fish are on the way, as evidenced by continuing reports of salmon being caught in the Mokelumne below Interstate Five, the South Fork Mokelumne and Hog and Beaver sloughs.
“One of our hatchery employees, Jake Aucelluzzo, last weekend landed a bright 14-pound salmon while fishing a Rat-L-Trap for striped bass in Hog Slough,” Smith said.
The steelhead numbers reported to date are behind those of last season’s record run. To date, the hatchery has counted 116 adult steelhead and 227 half pounders (juveniles). That compares to 406 adults and 34 juveniles last season to date.
A record for the number of steelhead returning to the Mokelumne River Fish Hatchery in one season was set earlier this year. The hatchery trapped 530 adults and 638 juveniles, a total of 1,168 fish. That compares to 719 adults and 402 juveniles the previous season, a total of 1,121 fish.
Factors behind the record salmon and steelhead runs in recent years include stronger river pulse flows by EBMUD, closures of the Delta Cross Channel gates, the use of tagging data to increase fish survival when released, barging salmon, habitat improvements, the rebuilding of Woodbridge Dam and the 1998 Lower Mokelumne River Settlement Agreement. Information: (209) 759-3383.
The river is running through it/The Carmel River near Paso Hondo Road in Carmel Valley
November 3, 2018
Monterey County Herald By Rodrigo Pérez Ortega (Tommy Williams/Lee Harrison)
In the process of removing the San Clemente Dam in 2015, workers created a pristine route for the Carmel River, complete with step pools and nicely arranged boulders.
Winter floods have since transformed the river route into anything but pristine, but the “messy” course has been good for the native steelhead.
Lee Harrison, a research hydrologist at the National Oceanic and Atmospheric Administration’s Southwest Fisheries Science Center, studied how four major floods boosted the river’s natural processes and improved the spawning habitat for the trout since the dam removal.
“The river structure has become more complex,” he says, and that’s mainly due to large wood and coarse gravel that has drifted from upstream.
The effects of the removal on the river were expected, but “the main uncertainty was how quickly the changes were going to occur,” Harrison says.
“It reset the system,” says Tommy Williams, a fishery biologist at NOAA. “It’s supposed to be messy, it’s supposed to be diverse.” For him, the floods were a boost for habitat recovery.
Built in 1921, the 105-foot-high San Clemente dam was taken down in November 2015 after it was determined that it posed a major public hazard since it could fail during an earthquake or a major flood. It is the largest dam removal in California to date, and the $84-million project offered a unique opportunity for scientists to study the impact of the removal on the river and the ecosystem it sustains. This is the first time these types of studies have been carried out on a river in a Mediterranean climate.
The federally protected steelhead trout are very dynamic and they don’t do very well in static environments, according to Williams. They are also very resilient and they are used to changes in their ecosystem when they migrate from freshwater to seawater and back.
The dam was hampering the spawning habits of the steelhead. Although they had a ladder that allowed them to swim upstream while the dam was in place, it was too steep and wasn’t ideal, says Doug Smith, a geomorphology professor at CSU Monterey Bay.
What was novel in this removal project was the management of the reservoir sediment. To avoid having the sediment that accumulated over the years to flow all at once and cause damage to the river and urban areas downstream, as had happened in the other dam removals, engineers decided to sequester it by building a dike and rerouting the river to the smaller San Clemente creek for a short stretch, where the improved fish passage was also put in place.
However, the neatly designed steps and pools for the wildlife passage were washed away by winter floods and no original structure is left. But the steelhead still managed to swim up and build fish nests, called redds. Scientist have now seen young fish of different sizes, indicating that the population is more diverse.
For now, there are no plans to restore the passage so long as wildlife continues to be able pass.
The steelhead were not the only ones who managed to swim up. Pacific lamprey has appeared upstream for the first time in 20 years. “Lampreys are supposed to be there,” says Smith. But non-native species have also flourished upstream, like the striped bass that eat the young steelhead. “It’s a real concern,” says Williams.
The dam removal has also helped other native animals to thrive. The endangered California red-legged frog lives upstream. Before the removal, the reservoir was a great habitat for the bullfrog, an invasive species that eats the red-legged frog. Now, with the dam gone, the number of bullfrogs has decreased. .
Downstream, the river is also physically changing. Some portions are now shallower because of the amount of sediment, but Smith expects it will wash through with future floods and “we’ll be left with very nice gravel,” he says. “But that depends on the time and how big the storms are in the next winter.”
In terms of seismic risk, the dam removal “was a huge success,” says Smith. “But I wouldn’t consider the river fully restored,” says Harrison. “There’s another dam –– the Los Padres dam –– that’s still in place upstream in the Carmel river.” There are talks of removing that dam in the future, but no decision has been made.
As they structurally age and reservoirs fill up with sediment, more dams will come down. “Each of them is an experiment,” says Smith, “and we get to see the environmental response and how quickly the physical landscape and the species adapt to the new sediment, the new water.”
There are more than 15 scientists working on different research projects in the area and everyone is excited about the next wet season. “What a great opportunity to study a large-scale, real-world issue,” Smith says. “And it’s right in our backyard.”
Snorkeling With The Salmon In A Northern California River
November 1, 2018
OPB/KUOW By Aaron Scott
It’s a rare person who would look at a wicked stretch of whitewater rapids and think: “Man, that’d make for some killer snorkeling.”
But that’s exactly what’s attracts nearly a hundred people to the Salmon River in Northwestern California every year.
The Salmon River Fish Dive is organized by the Salmon River Restoration Council and the U.S. Forest Service. Volunteers and professional biologists spend the day snorkeling the entire length of the Salmon River and its tributaries — more than 80 miles of river in all. Their goal is to count every single Spring Chinook salmon and Steelhead adult fish.
In the world of biology, it’s rare to survey an entire population — it’s just a lot of work. But they do it here because it’s such an important and threatened run, with important implications for the entire Klamath Basin, including the upper watershed that originates in Oregon. And they’ve been doing it for 24 years, which makes this one of the longest running and most comprehensive fish surveys on the West Coast.
At the crack of dawn on a midsummer day, survey participants gathered at the Forks of Salmon Elementary School and divided into small teams to divvy up the watershed. Each 3- to 4-mile reach was ranked by difficulty. The most dangerous stretch was claimed, as it is every year, by a Salmon River lifer: Will Harling, director of the Mid Klamath Watershed Council.
Harling’s team consisted of biologists Sophie Price and Allen Crockett and, for the first time, his 14-year-old son, Owen.
“Owen, I’m really excited: this is your first run on our home river,” said Harling, as he circled them up on the rocky shore at the top of their stretch. “French to Matthews is one of the most dangerous reaches on the river."
“And beautiful,” added Price.
“And beautiful,” Harling echoes. “Deep pools, big waterfalls.”
That is, beautiful pools, waterfalls and rapids that the team would have to navigate through steep mountain valleys with no cell service and only occasional road access, meaning they had to carry everything they’d need in their packs, and should someone get hurt, it was going to be a hard hike out.
But that didn’t stop Harling from diving goggles-first into the first winding rapid, as his teammates climbed over boulders alongside, before jumping in to join him in the pool below.
Harling explained the general process of the survey: “We have to walk around the rapids. Sometimes you can float through, and it’s kind of a judgment call if you know whether it’s safe or not. And one person will flush out the bubble curtain in case fish are hanging up in the bubbles, and then we go through the hole.”
“You definitely get a little banged up going down rapids, if you’re going down the exciting ones,” Price said. “My personal strategy is wearing a really thick wetsuit, and then I always have my hands out in front a my face, because you often dive straight into a bubble curtain, and then you also can’t see anything, so it’s extra exciting.”
In bountiful years, they compare counts at the bottom of each pool. But this year, with the exception of one pod of five spring chinook, the fish were proving elusive, forcing the divers to search under ledges and boulders in the hopes of finding single fish seeking refuge. By late afternoon, their tally was only 14 adult springers and eight steelhead.
For Harling, the salmon are much more than just numbers: they’re practically family. He was born just up the river’s banks in an old mining cabin.
“When I was a kid growing up on the Salmon River, fishing for spring chinook salmon was a way a life — pretty much every hole had fish in it,” he said. “But in the mid-’80s, that changed, and all of a sudden the salmon were dying from a thousand cuts: from the legacy of mining, from the legacy of logging, and then finally from the droughts.”
While populations vary from year to year, biologists have documented that the spring runs here have generally fallen from thousands of fish to hundreds — a general downward trend shared by many West Coast salmon runs.
“Historically, spring salmon were the largest run and contributed the greatest biomass: feeding people, feeding animals, and feeding and providing the foundation of many of our food webs in the river systems,” said Frank Lake, a research ecologist at the U.S. Forest Service Pacific Southwest Research Station. “The loss of that literally means a near collapse of all those other things that depend upon them.”
Local tribes and organizations have been pushing for the spring chinook to be listed as endangered for years — to no avail. The government has argued the springers were no different from the fall chinook, which have bigger remaining runs. But recent genetic research has proven that the spring chinook are indeed their own species, and local groups, such as the Karuk Tribe and the Salmon River Restoration Council, have resubmitted a petition for an endangered listing.
The population’s decline has consequences that reach far beyond the local ecosystem, too. The Salmon River flows into the Klamath River, which has its headwaters in Oregon, and this population is one of the last wild runs left in the entire Klamath Basin, where dams are slated to be removed beginning in 2020.
“The importance of spring salmon here is that when the dams are removed on the Upper Klamath, it has the potential to be that genetic security that comes back into the Klamath Basin system,” Lake said.
But that depends on whether those salmon can be conserved.
The shadows were growing long by the time Harling and his team finished their reach.
Any hope that other teams might’ve fared better evaporated as they returned to the elementary school. The final count came in at 168 spring chinook adults and 164 steelhead adults in all of the Salmon River watershed, making it the third-lowest year on record.
Harling holds out hope that removing the Klamath River dams, other conservation measures such as restoring fire to the land, and the protections that would come with an endangered species listing could help the spring chinook rebound. Because the idea of a Salmon River without salmon — it’s just unimaginable.
“It makes me feel sick in my stomach,” he said. “I wouldn’t want to be alive if my kid couldn’t fish in the salmon river — wouldn’t be able to see salmon. It’s part of who we are. We got to keep the faith, because what else is there.”