The Top Reason for the Delta Ecosystem Collapse: Massive Water Exports South

Do you want to know why Delta smelt, longfin smelt, imperiled Chinook salmon, green sturgeon and other fish species in the Sacramento-San Joaquin River Delta are on the edge of extinction?

It just might have something to do with the fact that huge amounts of water have been exported out of the Delta for decades, combined with the impacts of toxics, pollution, invasive species and climate change.

You can check out the annual exports out of the Delta by state and federal water projects over the 23 years from 2010 to 2023 in the chart below this article. Data wasn’t available yet for 2024 and 2025. These figures are in million acre feet of water. You can view the tables on the Delta Stewardship Council website: viewperformance.deltacouncil.ca.gov/...

Advocates for the San Francisco Bay-Delta say 3 million acre feet of water in a year is the maximum amount of water that can be exported out of the Delta without causing catastrophic harm to salmon, steelhead, Delta smelt, long fin smelt and other fish.  

Yet you can see that during the vast majority of years, 19 out of 23, the amount of water delivered to the south of the Delta contractors by the Central Valley Project (CVP) and State Water Project (SWP) has been significantly higher than 3 million acre feet, starting with the expansion of almond and other thirsty crops in the early 2000s. 

The Pelagic Organism Decline (POD) was first documented by state and federal scientists in 2005. As you can see, 2011 set an all time record for combined state and federal water exports with 6.69 MAF (million acre feet) pumped out of the Delta. 2017 was another huge year for Delta water exports, with 6.46 MAF delivered to state and federal water contractors.

Water exports only went below 3 million acre feet of water in four critically dry drought years — 2014, 2015, 2021 and 2022.  

Water managers reduce export targets in dry years and increase them during wet years. In 2023, the last year the council recorded on its website, 5.39 MAF of water was delivered to agribusiness and Southern California water agencies from the state and federal pumping facilities.

The Sacramento-San Joaquin River Delta is in biggest-ever ecological crisis. While the salmon returns to the Sacramento River and its tributaries have been better this year than during the previous two years, the improved returns come after unprecedented three year closure of the commercial salmon fishery off the California coast and the third year of a complete closure of the main stem Sacramento to recreational fishing, due to the collapse of the Sacramento fall-run Chinook salmon population. 

Of course, other factors have contributed to the ecosystem crash, including toxics, pollution, upstream diversions, and the proliferation of invasive species, most recently the golden mussel infestation in Delta waters. But none figure more prominently in the crash than the water export regime that has reengineered the hydrology of the Delta to serve corporate agribusiness operators like the Resnicks, the largest orchard fruit growers in the world, who own hundreds of thousands of acres of land in Kern County and elsewhere. 

The Delta smelt, an indicator species that was once the most abundant fish in the estuary, has become functionally extinct in the wild. The California Department of Fish and Wildlife has found not a single Delta smelt in its Fall Midwater Trawl survey throughout the Delta in 7 years: apps.wildlife.ca.gov/

A peer-reviewed article published in 2016, “Delta Smelt: Life History and Decline of a Once-Abundant Species in the San Francisco Estuary” in the San Francisco Estuary and Watershed Science journal 14(2), explains the smelt’s decline succinctly: ca.water.usgs.gov/… 

“A major driver of decline is change to the Delta ecosystem from water exports, resulting in reduced outflows and high levels of entrainment in the large pumps of the South Delta,” wrote authors Moyle, Peter B., University of California, Davis Brown, Larry R., U.S. Geological Survey Durand, John R., University of California, Davis Hobbs, James A., University of California, Davis. “Invasions of alien species, encouraged by environmental change, have also played a contributing role in the decline. Severe drought effects have pushed Delta Smelt to record low levels in 2014–2015. The rapid decline of the species and failure of recovery efforts demonstrate an inability to manage the Delta for the ‘co-equal goals; of maintaining a healthy ecosystem and providing a reliable water supply for Californians. Diverse and substantial management actions are needed to preserve Delta Smelt.”

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 charts in this May 2025 CDFW memo illustrate how dramatic the declines in Delta pelagic (open water) fish populations have been over the years: nrm.dfg.ca.gov/...

In a statement in January of this year regarding the listing of critical habitat for endangered Longfin smelt, Dr. Jon Rosenfield, science director for the San Francisco Baykeeper, pointed out the critical role that freshwater flows play in the Bay-Delta ecosystem.

“Like most of the Delta’s native fishes, longfin smelt need high river flows to reach San Francisco Bay in the winter and spring,” said Rosenfield. “The mixing in the Delta of fresh and salt water creates the habitat that smelt, salmon, sturgeon and countless other fish depend on for survival. Continued unsustainable diversion of water threatens to extinguish the Bay’s longfin smelt and other native fish.”

As the San Francisco Baykeeper documented in April of 2024, the state and federal pumping facilities in the Delta often exceed their take limits for winter-run Chinook salmon and Central Valley steelhead “protected” under the Endangered Species Ac: baykeeper.org/...

“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. Since December 1, 2023, an estimated 2,919 naturally spawned 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,” the Baykeeper reported.

A Sacramento Bee analysis of data from the CDFW in 2024 further documents the carnage in the export pumping facilities: since 2002, state and federal water pumping from the Delta killed an estimated 600,000 Chinook salmon and 50,000 steelhead trout: ncgasa.org/… 

To give you an idea of the fish mortality that can be caused by the operation of the Delta pumping facilities, in May of 2011 I documented the slaughter of 1.6 million Sacramento splittail, a native minnow found only in the Sacramento-San Joaquin River watershed, in just three days in the Delta “fish salvage” facilities in just three days: www.biologicaldiversity.org/… 

From just January 1 to Aug. 2 of that year, an astounding 8,966,976 splittail, 35,556 chinook salmon, 430,289 striped bass, 54,412 largemouth bass, 69,383 bluegill, 76,570 white catfish, 28,301 channel catfish, 233,174 threadfin shad, 264,171 American shad, 1,642 steelhead and 51 Delta smelt were “salvaged” in the state and federal water export facilities from January 1 to August 2, 2011, according to Department of Fish and Game (DFG) data.  

Just envision the many millions of splittail, winter-run Chinook salmon, spring-run Chinook salmon, fall-run Chinook salmon, Delta smelt, green sturgeon, white sturgeon and other native fish killed in the Delta pumping facilities since 1967 and you get an idea of the toll these pumps take on both native species and introduced species including striped bass, threadfin shad, Japanese pondsmelt and American shad.

Finally, it was no surprise that the slaughter of these 8.9 million native fish and hundreds of thousands of salmon, steelhead and other fish species took place in 2011, an all-time record year for combined state and federal water exports with 6.69 MAF (million acre feet) pumped out of the Delta that year. The state and federal water projects have exceeded 6 MAF — the equivalent of 6 Folsom Lakes — in annual exports 6 times since 2000, as the data from the Delta Stewardship Council reveals.

While other factors such as pollution, toxics, invasive species and climate change definitely compound the environmental destruction caused by export pumping on the Delta, it is the diversion of Delta water through the state and federal pumping facilities on the Delta that tops the list of killers of imperiled salmon, steelhead and other fish species in the Bay-Delta estuary.

The data below was compiled from the Delta Stewardship Council website:   

  Water Year                          Year Annual Export       15 Year Average