Gary Reedy, senior river scientist with the South Yuba River Citizens League, shows a salmon carcass to members of a rafting tour down the Yuba River last weekend. They monitor the number and condition of carcasses to measure the health of the returning Chinook salmon population.

Federal officials have sounded the alarm that for the second year, winter-run Chinook salmon could lose almost the entire class of juveniles due to high temperatures in the Sacramento River. That announcement could have dire implications on next year's water supply and the future of the species.

But water district managers in the Sacramento Valley cautioned it was too early to draw such conclusions, while wondering if the sudden announcement was part of a larger strategy to justify cuts to 2016 water deliveries.

The National Marine Fisheries Service announced in a media conference call the number of juvenile winter-run salmon, an endangered species, counted at the diversion dam in Red Bluff was 22 percent lower than last year as of Oct. 21, an ominous sign given that 95 percent of hatched juveniles died in 2014 due to warm temperatures in the Sacramento River.

"The numbers look quite bad this year," said Maria Rea, the agency's assistant regional administrator. "They are a lot worse than we've been anticipating."

The data shows a steep drop over the past five years in the number of juvenile winter-run salmon counted at Red Bluff as the species heads down the river towards the ocean.

In 2009, an estimated 4.4 million juveniles passed Red Bluff. By 2014, that number had dropped to 411,000, a testament to the devastating impacts of the drought. So far in 2015, an estimated 217,000 have been counted.

The numbers seem to suggest that a controversial plan to avoid a repeat of 2014's massive mortality event failed. In May, the U.S. Bureau of Reclamation realized that temperature models for the cold-water pool in Lake Shasta were wrong, prompting the agency to withhold water deliveries, which farmers and cities were counting on, in order to preserve cold water for winter-run Chinook.

"We knew it was a high-risk plan because it deliberately exposed eggs to higher temperatures than normal," Rea said. "That resulted in operations that were hard on farmers and hard on fish. The drought has forced us into very difficult choices."

Salmon have a three-year spawning cycle, so a third consecutive year of high mortality could put the species on the brink of extinction, Rea said.

A conservation hatchery below Shasta Dam for winter-run Chinook on the Sacramento River does provide a buffer against extinction, Rea said.

"But the really large impacts to wild populations could bring it back to very low levels and undo decades of hard work put in towards recovering the species," Rea said.

Local water managers respond

Sacramento Valley water district managers, however, cautioned it is premature to draw any conclusion from the Red Bluff counts. They pointed out that there are still two months left in the outward migration season.

Thad Bettner, general manager of the Glenn-Colusa Irrigation District, said the salmon are likely still pooling together near Redding because they have not received natural signals to start migrating south and pass by the Red Bluff diversion dam.

"We haven't seen any indicators of flow or turbidity that tell the fish to move out of the system," Bettner said. "We're a little disappointed that NMFS had to come out with information (Wednesday) because the story is still developing."

Impacts on 2016 water supply

Lewis Bair, general manager of Reclamation District 108, said the announcement was a surprise and wondered if the agency was trying to set the stage to justify water supply cuts in 2016.

"It worries me that it might be a strategy to help support the decision on what they're going to do next year," Bair said. "(Rea) is starting dialogue that creates concern. Everyone will read that the fish are troubled. Why would she do that?"

"The out-migration pattern continues through December, and you don't expect fish to really start moving out until you have your first rainfall," Bair continued. "And she's making a statement about how they did, and I have no idea how she's doing that."

When these concerns were posed to Rea, she said there would have to be a dramatic improvement in the numbers to not have a high level of concern.

"We're two-thirds of the way through the migration window. Even if the count doubles, we still would have a very significant concern," Rea said. "We hope to see well over a million juveniles, and that seems unlikely given where we are at this point in the season."

Rea also noted the numbers so far this year are preliminary.

Bair said growers in his district are already prepping for another round of cuts in next year's water deliveries.

"We need better-than-average rain to get average water supplies," Bair said. "Fish are first in line. They're going to get water first. If there's anything left, it will go to agriculture and people."

Rea said that the salmon counts are one of the pieces of information that will factor into 2016 water deliveries.

"We'll have to be very conservative to see what type of operations will be necessary to run a cold water pool," Rea said. "We have to make sure the third year (of winter-run Chinook) is protected."

Anglers, activists await spawning season

Government officials, anglers and activists are watching closely as the spawning season of the fall run of Chinook salmon approaches its height.

Reports of declining salmon populations in the Sacramento, Feather and Yuba rivers have the agencies, sportsmen and environmental groups that track the fish waiting anxiously for the post-spawn carcass counts.

Preliminary surveys from reporting stations at fish ladders on the Yuba and Feather rivers, and the Central Valley Angler Survey on the Sacramento and Feather rivers, hint at fewer salmon returning to the spawning waters than last year.

But Colin Purdy, an environmental scientist with the California Department of Fish and Wildlife, said it's too early to jump to conclusions.

"The numbers appear a little bit lower than last year, but the important qualifier to that is fish might be showing up later than they normally do because of the drought," Purdy said. "It could be a little bit of both."

By counting carcasses over the course of the next few months, biologists will have a better idea of how the fall run population fared in the fourth year of the drought.

"It's hard to know what the management implications of these early numbers are, and it's hard to speak to it with any authority," Purdy said.

The fall run of salmon is the largest of the four species of Chinook in the Central Valley and is open for anglers to harvest from July 16 to as late as Dec. 16, depending on the location. The spring run is listed as threatened, and the winter run is listed as endangered by the federal Endangered Species Act.

Feather River

The Feather River Hatchery in Oroville is one of five major hatcheries in the Central Valley region and is one of the best places to view Chinook spawn, even with smaller numbers of salmon passing through so far.

As of Oct. 26, the hatchery reported 12,626 returning salmon, down from 16,752 at the same point in 2014, but there are about two weeks remaining in spawning season at the location, hatchery manager Anna Kastner said. The facility has a viewing window at the fish ladders, a place to see hatchery staff taking eggs from salmon and a platform overlooking the river where salmon can be seen jumping. A short hike from the hatchery, salmon spawning grounds can be viewed from the banks of the river, however the best way to see the salmon redds (depressions in the river floor made by female salmon to lay eggs) is by kayak, Kastner said.

"We're past our peak. I hear fish are coming in, but we haven't seen many of them yet," she said. "Things do look different to us than in the past few years. The salmon are trickling in, a little smaller and with fewer eggs."

Anglers largely avoided fishing for fall run salmon on the Feather River this year, but it had less to do with the number of salmon in the river and more to do with the river conditions, said James Lyons, of the Department of Fish and Wildlife's Central Valley Angler Survey.

Changes in water released from the Oroville Dam, and less water released from the Thermalito Afterbay Outfall, meant the cool pool of water at the northern end of the area open to fishermen was absent this year. The salmon moved up stream and out of the reach of anglers, Lyons said.

Yuba River

There is a relationship between the salmon counts on the Feather and Yuba rivers, and this year the water temperature and flow ratios lined up so that many of the fall run Chinook bypassed the Yuba River, said Gary Reedy, river science director with the South Yuba River Citizens League.

"You'd have to go back into the 1980s to find a year where the Yuba River flowed as low and as hot at its confluence as it did this year," Reedy said.

For a fish that likes cold water, that meant many salmon stayed in the Feather River, which helped lead to much smaller numbers of Chinook at the Daguerre Point Dam salmon ladder near Hammonton, Reedy said.

In September, 378 salmon climbed the ladder at Daguerre Point Dam, down from 896 the previous year. Through the first 19 days of October, 329 salmon passed that point, well shy of the pace that sent 3,144 over the dam during the entire month of October in 2014.

However, the numbers at the counting facility do not tell the whole picture, Yuba County Water Agency projects manager Geoff Rabone said. Salmon typically return to their spawning grounds after spending two to four years in the ocean.

"Ocean conditions and temperatures also play a role," Rabone said. "It's a complicated issue, and we won't know the whole story until we get more complete numbers."

The best place to watch the salmon on the Yuba River is at Hammonton Grove Park, where a bluff overlooking the river is a short walk from the parking lot, Reedy said. SYRCL also offers salmon tours, including raft trips on Saturday and Nov. 7 to spawning waters, and a walking tour on Nov. 15.

Sacramento River

Fall run salmon fishing on the Sacramento River is the lifeblood for many commercial guides, and the conditions forced many to look north to find the fish.

Scott Feist of Feisty Fish Guide Service in Yuba City took his boat out nearly every day from July 16 to Oct. 20. He was still able to catch his limit, most of the time, by moving farther up river.

"For the guys who knew what they're doing, and knew the right areas to go into, it was pretty decent," Feist said. "Not screaming limits like it has been in years past but it was still quality fishing."

During a normal year, the salmon tend to pool between Hamilton City and Woodson Bridge, near Corning, before moving into tributaries or north of Redding to spawn, but this year they congregated between Los Molinos and Jellys Ferry near Bend, said James Lyons of the Department of Fish and Wildlife's Central Valley Angler Survey.

"The harvest was definitely less than last year. Guides had a tough time. Everybody had a tough time," Lyons said. "A lot of times the guides were still catching fish, but they weren't catching as quickly or getting the limits like they used to."

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