Dead fish wash up near $6.3 million passageway designed to protect them. Why didn’t it work?

Dozens of fish carcasses — 13 of them Chinook salmon protected by the Endangered Species Act — rotted in the sun Tuesday a couple hundred yards from a new $6.3 million structure that state officials built specifically to keep that grisly scenario from happening.

Before the winter and spring flood season this year, engineers completed work on the new fish passage along the Fremont Weir, a nearly two mile-long concrete structure atop the Yolo Bypass. The bypass is a 40-mile long engineered flood plain that starts near Woodland and shunts flood waters from the Sacramento River into agriculture fields.

The fish passage was intended to keep fish from becoming stranded along the weir and in the bypass once the flood waters receded back into the Sacramento River’s main channel. An automated gate was supposed to open once water levels got high enough to overflow into the bypass, allowing fish to swim back into the Sacramento River.

But in February, state officials who manage the facility noticed it wasn’t working right. Too much water was pouring through the passage, eroding the structure. Officials had to close the gate almost entirely, meaning fewer fish could escape.

The Department of Water Resources is now facing an expensive upgrade to an already multimillion structure to make it ready for the next rainy season — and prevent what happened this week.

“Yesterday was the day of carnage,” Chris McKibbin, a regional fisheries biologist for the Department of Fish and Wildlife, said on Tuesday afternoon as he slowly walked with 11 state biologists in waist-deep water pushing a large net corralling fish along the Fremont Weir’s western stretch.

Over the weekend, someone called a poaching tip line to alert state wildlife officers that fish were stranded in the receding waters along the weir, McKibbin said.

When a team of biologists arrived on Monday to rescue the fish, they were too late for dozens of them. The biologists found the dead adult salmon, plus at least two dead white sturgeon, more than two dozen striped bass carcasses and other dead fish.

The optics of the dead fish rotting next to the new facility raises fresh questions about whether habitat restoration programs championed by former Gov. Jerry Brown’s administration, through his controversial Delta tunnels project, will be completed in time to make a difference. The programs are designed to prevent the extinction of numerous species of fish whose plummeting numbers in recent years have lead to wide-ranging cuts to California’s water supply.

The erosion and design problem at the Fremont Weir facility comes after the Department of Water Resources has faced more than two years of withering criticism for allowing problems to fester at Oroville Dam, which suffered catastrophic damage when its spillways failed in 2017. Investigators cited decades of faulty design and maintenance.

Department of Water Resources spokeswoman Erin Mellon said the setback at the Fremont Weir is a small one that shouldn’t detract from the important work state officials are doing to help the state’s struggling fish populations. She said lessons learned from this winter’s problems at the new passageway will be used to ensure they don’t happen elsewhere.

“We’re always trying to tweak and improve our projects to address either known or unknown design issues to make them operate even better,” she said.

The Fremont Weir, built in 1924, has long been a death trap for imperiled native fish such as green sturgeon, steelhead trout and Chinook, whose various runs are protected under state and federal endangered species laws. Fish that migrate into the flood waters of the bypass think it’s part of the Sacramento River’s natural flood plain.

When the river recedes, fish become stranded in the shallow, rapidly-disappearing water that forms in the L-shaped lip at the bottom of the 1.8 mile-long concrete Fremont Weir.

Over the years, biologists with McKibbin’s agency have staged numerous rescues after the flood waters recede to try to save as many fish as possible before the water dries up or they’re caught by poachers.

After finding the dead adults on Monday, McKibbon and his team were able to rescue some 700 tiny juvenile fish along the weir adjacent to the new passageway. They rescued several dozen more adult and juvenile fish on the weir’s western section, which isn’t connected to the new structure.

McKibbin said the dead adult salmon his team found this week were likely spring run Chinook, which are listed as threatened under the federal Endangered Species act, or winter run, which are among the most critically endangered fish in California.

During California’s last drought, warm, low waters of the Sacramento River proved particularly lethal to the winter run Chinook, prompting regulators to cut the water supply for farms and cities across the state.

People caught killing endangered fish would face hefty fines and prison time, but government agencies often are legally allowed to kill protected fish when they’re unintentionally trapped in California water infrastructure.

In May 2018, state and federal officials held a groundbreaking ceremony at a new fish passage project saying it would help stop fish from being stranded. The $6.3 million passageway is largely funded by the Department of Water Resources and the U.S. Bureau of Reclamation, the federal agency that manages dams and water-supply canals for the federal government.

McKibbin said the passage appeared to be working earlier in the flood season, when underwater cameras caught at least 12 sturgeon swimming through the new structure before the flows were reduced to prevent the erosion.

“It did pass some pretty big sturgeon,” he said.

The Fremont Weir project is politically sensitive because it’s one of more than two dozen projects in California EcoRestore — former Gov. Brown’s plan to improve fish and wildlife habitat in the Sacramento-San Joaquin Delta while the state forged ahead with his controversial Delta tunnels project.

The EcoRestore habitat plan — which was seen as a way of appeasing critics of the multibillion-dollar Delta tunnels project — became controversial because of downsizing. The state initially said it would spend $8 billion to restore 100,000 acres of habitat. In 2015, Brown reduced that to 30,000 acres and $300 million. The state later committed to restoring an additional 1,800 acres.

The tunnels project — which the state says will protect fish while improving the reliability of water deliveries to the southern half of the state — is now in limbo. Gov. Gavin Newsom said he’d reduce the twin tunnels to a single tunnel. The state continues to move ahead on the habitat work.

For instance, officials are planning in the coming years to build at least two similar passageways along the Frement Weir to ensure even more fish can move back and forth from the river. The new facility is an important test to ensure those passageways and others around the state work correctly, said Kristopher Tjernell, a deputy director at the state Department of Water Resources.

“The bottom line is we’ve actually put a facility in this known man-made impediment to fish passage,” Tjernell said. “And we’re finally going to be able to solve this issue so we can ... see wild populations come back.”

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