Sacramento River and Delta fish populations are in worst-ever crisis as pumps keep exporting water to Big Ag

Central Valley salmon and Delta fish populations are in their worst-ever crisis ever as the California Department of Water Resources (DWR) moves forward with the controversial Delta Tunnel, Sites Reservoir and voluntary water agreements.

Ocean commercial and recreational fishing and river recreational fishing for salmon has been closed for the past two years, due to the collapse of Sacramento and Klamath River salmon populations. The 2024 stock abundance forecast for Sacramento River Fall Chinook, usually the most abundant stock in the ocean fishery, was only 213,600 adults.

The return of fall-run Chinook salmon to the federal Coleman National Fish Hatchery on Battle Creek in Fall 2023 was a disaster, with the hatchery officials forced to obtain eggs from the state’s salmon and steelhead hatcheries.  

This fall’s return of salmon to the Coleman Hatchery was shockingly low again, even with the second year of the salmon fishing closure in place. The normal production at the hatchery is 12 million juvenile fall Chinook salmon; this year they collected approximately 5.4 million eggs at the hatchery, according to the hatchery’s Facebook page. Again, they had to obtain eggs from the Feather River, Nimbus and Mokelumne River hatcheries to meet their production goal.

In contrast, more than 30,000 fall-run Chinook have been counted to date on the Mokelumne River with hundreds more arriving daily from the Pacific Ocean to spawn. “This is the largest salmon return on the Mokelumne since record keeping began in 1940, surpassing the record-setting 2023-24 total count of 28,698 Chinook with several weeks still left to go in this spawning season,”  EBMUD wrote. (www.ebmud.com/...)

However, the Mokelumne River is a tributary of the San Joaquin River, not the Sacramento. The big numbers of fish reported there are not included in crafting ocean and river salmon fishing seasons, since the seasons are based on the Sacramento River Index.

Endangered Sacramento River spring and winter-run Chinook also continue their march towards extinction. The spawning escapement of Sacramento River Spring Chinooks (SRSC) in 2023 totaled 1,479 fish (jacks and adults), with an estimated return of 106 to upper Sacramento River tributaries and the remaining 1,391 fish returning to the Feather River Hatchery: www.pcouncil.org/…

Butte Creek spring-run Chinook run was lowest ever 

The return to Butte Creek of just 100 fish in 2023 was the lowest ever. In 2021, an estimated 19,773 out of the more than 21,580 fish total that returned to spawn in the Butte County stream perished before spawning.

While the numbers of salmon returning to the Sacramento and Klamath rivers and their tributaries this year won’t be made public until the data is posted on the Pacific Fishery Management Council’s website in late February 2025 in preparation for the crafting of salmon seasons in March, we do know that the return to Butte Creek this year was abysmal. 

Only 51 spring Chinooks were reported in the Butte Creek snorkel count and “probably less than 25” in the carcass count, according to Allen Harthorn, executive director of Friends of Butte Creek. 

Nor did the winter run, listed under the state and federal Endangered Species Act, do well. Spawner escapement of endangered Sacramento River Winter Chinook (SRWC) in 2023 was estimated to be only 2,447 adults and 54 jacks, according to PFMC data.

A group of us, including the late conservationist and Fish Sniffer magazine publisher Hal Bonslett, successfully pushed the state and federal governments to list the winter run under the state and federal Endangered Species Acts starting in 1990-91 because we were so alarmed that the fish population had crashed to 2,000 fish.

Then in 1992 the run declined to less than 200 fish. Even after Shasta Dam was built, the winter run escapement to the Sacramento River was 117,000 in 1969.

Now we are back to approximately the same low number of winter-run Chinooks that spurred us to push for the listing of the fish as endangered under state and federal law over 30 years ago.  

The State Water Project (SWP) and Central Valley Project (CVP) Delta “death pumps” have been the biggest killers of salmon, steelhead, Sacramento splittail and other fish species in California for many decades, as I have documented in hundreds of articles in an array of publications.

Groups urge state and feds to stop killing steelhead, salmon in Delta pumps 

Earlier this year, a coalition of fishing and conservation groups, including the Golden Gate Salmon Association, San Francisco Baykeeper and Bay Institute, urged the state and federal water agencies to “take immediate action” to stop the unauthorized killing of thousands of Chinook Salmon and Steelhead at the State and Federal water export pumps in the Sacramento-San Joaquin River Delta: www.dailykos.com/...

Both winter-run Chinook salmon and Central Valley steelhead are protected under the Federal Endangered Species Act (ESA). Central Valley winter-run Chinook Salmon are also protected under the California Endangered Species Act (CESA).

The coalition reported that this is the second time in 2024 the coalition has responded to an increase in killing of legally protected fish at the pumps of the State Water Project and the Central Valley Project.

While the National Marine Fisheries Service (NMFS) has called for significant reductions in the Projects’ Delta water pumping, the California Department of Water Resources and the federal Bureau of Reclamation that own and operate the Projects “ignored these recommendations and continued to export water at rates that killed thousands of imperiled fish,” the groups said in a statement.

“Indeed, over the past week, DWR and Reclamation further increased pumping – as a result, significantly increasing take of winter-run Chinook Salmon at the pumps,” the groups wrote. “As a result, the water projects have exceeded the legal limits for killing both Central Valley Steelhead and winter-run Chinook Salmon established under the ESA by NMFS.”

State Water Project pumping accounts for 80% of the water exported from the Delta at this time, according to the groups.

The annual ESA take limit for winter-run Chinook Salmon is 1,776 fish. As of March 25, 2024, an estimated 3,030 winter-run had been killed at the pumps – not counting the much larger number of fish that likely died after being drawn by pumping into inhospitable parts of the Delta, the groups said.

Since December 1, 2023, an estimated 2,919 naturally spawned Central Valley Steelhead have also been killed by the Water Projects. The maximum allowable ESA Steelhead take is 1,571 as a three-year rolling average or 2,760 in any single year. The numbers show that the Water Projects are in violation of both limits.

Delta smelt have become virtually extinct in the wild

Now we turn to Delta Smelt. For the sixth year in a row, ZERO Delta Smelt were collected in the California Department of Fish and Wildlife’s Fall Midwater Trawl (FMWT) Survey in the Sacramento-San Joaquin River Delta from September through December 2023.

Then this summer a weekly survey by the US Fish and Wildlife Service  targeting Delta smelt caught only one smelt. “A late April IEP juvenile fish survey (the 20-mm Survey) caught several juvenile Delta smelt in the same area,” noted fishery scientist Tom Cannon in his blog on the California Sportfishing Protection Alliance website: calsport.org/...  

Once the most abundant species in the entire estuary, the Delta Smelt has declined to the point that it has become functionally extinct in the wild. The 2 to 3 inch fish, found only in the Delta, is an “indicator species” that shows the relative health of the San Francisco Bay/Delta ecosystem.

With the start of the new water year on October 1, 2024, representatives of fishing and environmental groups blasted the California Department of Water Resources  and U.S. Bureau of Reclamation for cancelling the fall flow protections for the few remaining Delta Smelt.  

Current state and federal Endangered Species Act (ESA) permits require DWR and Reclamation to release a pulse of water through the Delta to the San Francisco Bay in September and October to improve habitat conditions for the listed Delta Smelt, according to a statement from environmental and fishing groups. This fall outflow requirement is only triggered in years when it is wetter than normal and is often referred to as “Fall X2.”

The groups said some of the state’s largest Delta water exporters wrote to the agencies this August, requesting the suspension of “Fall X2,” despite Delta Smelt populations collapsing to record low levels in recent years.   

“It is incredibly disappointing to see the Newsom and Biden administrations willing to implement Trump-era water policies,” summed up Ashley Overhouse, Water Policy Advisor with Defenders of Wildlife. “This decision marks a somber start to the new water year, undercutting years of collaborative work to ensure the best available science is informing our water management decisions.”

Meanwhile, the other pelagic species collected in the survey — striped bass, longfin smelt, Sacramento splittail and threadfin shad — continued their dramatic decline since 1967 when the State Water Project went into effect. Only the American shad shows a less precipitous decline.

Between 1967 and 2020, the state’s Fall Midwater Trawl abundance indices for striped bass, Delta smelt, longfin smelt, American shad, splittail and threadfin shad have declined by 99.7, 100, 99.96, 67.9, 100, and 95%, respectively, according to the California Sportfishing Protection Alliance.

The graphs in this CDFW memo graphically illustrate how dramatic the declines in fish populations have been over the years: nrm.dfg.ca.gov/…  

The data for this fall’s midwater trawl survey has not become available yet, but I will publish an analysis of the results as soon as it becomes available, probably in late December or early January.

The Pelagic Organism Decline (POD), as state, federal and independent scientists describe the collapse, has been caused by state and federal water exports out of the Delta to agribusiness and Southern California water agencies, combined with the impact of invasive species, toxics, pollution and other factors.

Despite the current Central Valley salmon and Delta fish crisis, the Newsom Administration is pushing the Delta Tunnel, Sites Reservoir and voluntary water agreements — projects that will divert even more water out of the Sacramento River for corporate agribusiness and Southern California water agencies — when what we really need is more water for fish and the San Francisco Bay-Delta.