State of the Estuary: Health of CA Delta Fish Rated "Poor" As Freshwater Flows Decline

A new scientific report published by the San Francisco Estuary Institute finds that  fish populations in the Sacramento-San Joaquin Delta are in “poor shape,” citing “poor freshwater conditions” and other factors behind the collapse.

The report, “State of the Estuary,” has provided a comprehensive assessment of the health of San Francisco Bay and the Delta for many years.

The Institute’s latest report confirms the dramatic decline of Delta fish species that is revealed in my story detailing the most recent results of the Fall Midwater Trawl by the California Department of Fish and Wildlife (CDFW).

The report gives a “poor” rating for the health of Delta fish species and a “good” rating for Bay fish species, based on abundance, species diversity, native fish composition and the distribution of native fishes. You can read the report here: www.ourestuary.org/...  

“Declines in native fish abundance and diversity are influenced by drought, 2025 reduced outflow, and poor recruitment for key species,” the report’s score card points out.

The report's executive summary states: "Native fish continue to do well in the Bay and poorly in the Delta. Poor conditions in the Delta are tied to reduced inflows, invasive species, and pollution, though wet years still bring rebounds near restored floodplains."  

The report documents the “poor freshwater conditions” in the Delta, the result of water diversions and dams that have “nearly halved freshwater flows.”

"Freshwater Flow conditions in the Estuary remain Poor and Declining,” the report affirms. “Reductions in freshwater flows have created chronic, artificial drought conditions in the Estuary.”  

“High-volume flood flows in winter and spring are less common, leaving juvenile fish and invertebrates without the floodplain habitat and low-saline waters they need to survive (see also Beneficial Floods). The once-dramatic differences in flow levels between the wet and dry seasons, and between wet years and drought years, have been reduced,” the report reveals.

The report says the most recent 20 years of data (2004-2023), 14 of 20 years scored in the “poor” range. That’s a complete reversal from the first 20 years of data, when 14 years scored as “good.” 

Zero Delta Smelt Found in California Fall Survey

The report’s assessment dovetails with the results of the CDFW’s Fall Midwater Trawl survey that is conducted at an array of locations throughout the Delta ever year.

For the eighth year in a row, the California Department of Fish and Wildlife has found no Delta Smelt in their annual Fall Midwater Trawl survey in the Sacramento San Joaquin Delta in September, October and November of 2025. The results for December haven’t been compiled yet.

The latest survey results are revealed in a December 22 memo from Margaret Johnson, Environmental Scientist Bay Delta Region, to Erin Chappell, CDFW Regional Manager: nrm.dfg.ca.gov/...

The smelt, once the most abundant fish in the entire Delta, is an indicator species found only in the Delta. It’s decline to virtual extinction in the wild is a symptom of a larger decline, the Pelagic Organism Decline (POD), of the once robust open water fish populations of the San Francisco Bay-Delta Estuary.

The smelt has been demonized as a “worthless minnow” by President Trump and corporate agribusiness interests in the San Joaquin Valley, while Tribes, environmental groups and fishing groups point to the key role that it plays in the ecology of the Bay-Delta Estuary.

Caleen Sisk, Chief and Spiritual Leader of the Winnemem Wintu Tribe, points out the enormously significant role that Delta Smelt play in California’s aquatic ecosystems.

”Delta Smelt are the thread that ties the Delta together with the river system,” said Sisk. “We all should understand how that affects all the water systems in the state. They are the irreplaceable thread that holds the Delta system together with Chinook salmon.” 

The species has been kept from total extinction only through a captive breeding program run by UC Davis in Byron in the Delta. In a cooperative project, the state and federal governments have released thousands of hatchery Delta Smelt back into the estuary. 

The monthly FMWT surveys were conducted Sept. 2-17, Oct. 1-16, and Nov. 3-18. During each of the three months, 130 fish trawls were conducted, except for one station in October, Johnson reported.  

“No Delta Smelt were collected at any stations from September through November,” Johnson wrote. “The 2025 September-November index (0) is tied with 2016 and 2018-2024 as the lowest index in FMWT history.”

However, she pointed out that the Enhanced Delta Smelt Monitoring (EDSM) survey of the U.S. Fish and Wildlife Service (USFWS) did find 31 Delta Smelt between October 6 and November 20, a period of seven weeks which comprised of 906 tows (U.S. Fish and Wildlife Service 2025).      

Most adult Delta Smelt are less than 3 inches long . They are nearly translucent, with a steely-blue sheen on their sides. They have a smell that similar to that of cucumbers. They usually live for just one year, spending their entire lives in the San Francisco Bay-Delta.

“As larvae, they start out eating microscopic food like unicellular algae, planktonic animals, and small crustaceans. As they grow, their diet shifts almost exclusively to small crustaceans called copepods,” according to the Center for Biological Diversity.    

The Delta Smelt’s dramatic decline is part of the larger Pelagic Organism Decline (POD) in the San Francisco Bay-Delta Estuary, first identified by state and federal government biologists in 2004. Along with the Delta Smelt, populations of Striped Bass, Longfin Smelt, Sacramento Splittail, and Threadfin Shad have crashed in the Delta in recent years: www.nceas.ucsb.edu/...  

Other Delta Fish Species Collapse 

Striped Bass:

Striped Bass, an introduced anadromous fish species that is popular with anglers that reached an estimated high of 3 to 5 million legal-sized fish in the 1960s, continued their precipitous decline.

“Seven age-0 Striped Bass were collected at index stations in September for an index of 6. In October, five were collected for an index of 5.In November 18 were collected for an index of 18. The 2025 September-November index (29) is a 68% decrease from the previous year,”  Johnson wrote.        

Longfin Smelt

The Longfin Smelt, a native fish species that is now a candidate for listing under the federal Endangered Species Act, showed a relatively small increase from the previous year’s survey, but the population is still at just a small fraction of historical levels.

“Zero Longfin Smelt  were collected at index stations in September, resulting in an index of 0. “In October, four were collected for an index of 4. In November, 60 were collected for an index of 133. The 2025 September-November index (137) is an 11% increase from the previous year. One Longfin Smelt was collected at a non-index station during the October survey,” Johnson noted.      

Threadfin Shad:

Threadfin Shad, an introduced fish species that was released by the CDFW as a forage fish for larger fish, declined even further from the previous year’s survey.

“One Threadfin Shad was collected at an index station in September for an index of 1. In October, two Threadfin Shad were collected for an index of 2. In November, five were collected for an index of 5. The 2025 September-November index of 8 is a 97% decrease from the previous year. A total of 915 Threadfin Shad were collected at non-index stations during September, 95 were collected in October, and 125 were collected in November,” Johnson continued.  

Sacramento Splittail:

Likewise, Sacramento Splittail, a native minnow that used to support a popular recreational fishery on the Sacramento River during high water years, were completely absent from the fish caught in the survey.

“No Splittail were collected at index or non-index stations in September through November for an index of 0. The 2025 September-November index (0) is a continuation of low to zero catch in recent years,” Johnson said.

She noted that the “Splittail FMWT index tends to be low or zero except in relatively wet years, such as 2011.”

American Shad:

The American Shad, an introduced anadromous gamefish, has not collapsed as precipitously as the other fish species, but they still are found well below the historical numbers that once migrated through the Delta.

“A total of 428 American Shad were collected at index stations in September for an index of 477. In October, 105 were collected for an index of 170. In November, 201 were collected for an index of 233. The 2025 September-November index (880) is a 8% increase from the previous year. 148 American Shad were collected at non- index stations during September, 67 were collected in October, and 55 were collected in November,” Johnson wrote.  

I encourage anybody interested in the collapse of once abundant fish species to read the entire memo and look at the graphs: nrm.dfg.ca.gov/…

Massive Water Diversions Spurred Delta Fish Collapse

The collapse of the Delta fish and salmon populations has been spurred by the export of vast quantities of water to corporate agribusiness interests in the San Joaquin Valley and Southern California water agencies by the State Water Project and Federal Central Valley Project for many decades. Other factors behind the collapse  include reduced river inflows into the estuary, toxics, pollution, increased water temperatures and invasive species.

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 data analyzed by the California Sportfishing Protection Alliance. Thus, you can clearly see that five of the once abundant fish species have declined by 95% to 100%.

Only the American shad has declined less, but still has plummeted below historical levels. These fish species all collapsed during my lifetime. 

Despite this ecosystem collapse, Governor Gavin Newsom continues to promote the environmentally destructive Delta Tunnel and Sites Reservoir, projects that will take even more water out of the Delta. While Newsom pushes these projects, President Donald Trump has directed the Bureau of Reclamation to export even more Delta water to benefit his corporate agribusiness donors and Southern California water agencies — when what the ecosystem desperately needs is less water exports, not more.