A vanishing number of Delta smelt in San Francisco Bay is finding a changing climate contributing to its declining numbers.

By Hanisha Harjani, Yale Climate Connections (CC BY-NC-ND 2.5)

Deep in the San Francisco Bay, two rivers splinter into a vague triangle, creating one of the richest watersheds in California. This estuary – the Sacramento-San Joaquin River Delta – is an important source of freshwater for the 4 million folks who live in the region. Local agricultural, fishing, and recreation industries bring in billions of dollars a year, and the area also provides a rich habitat for local wildlife. 

Over the past few decades, this watershed has seen a dramatic change in its climate. Years-long droughts and record-high temperatures have transformed the region – a shift that’s told no better, perhaps, than through the story of the Delta smelt.

The Delta smelt is an iridescent fish about the size of a finger. The fish is a bioindicator, often noted for its distinct smell of fresh cucumbers. Though small in size, it has an impact reaching beyond the Delta, all the way to Capitol Hill. The smelt’s role in Northern California’s decades-long “water wars” have made it a key player in shaping the region’s water policy.

A harbinger of threats to other species

As a bioindicator, its presence in the Delta signifies a healthy ecosystem – one that can support a diverse range of life. However, not since the 1980s have the fish been abundant in the wild.

To Tien-Chieh Hung, PhD,  director of the Fish Conservation and Culture Laboratory (FCCL) at UC Davis, it’s simple: “If these fish are going extinct, then there are other species that are going to be listed as threatened or endangered, too.”

There was a time when these fish swam through the Delta in the thousands. Trawling surveys would pull up nets full of their thin, shimmering bodies. It’s now rare for these surveys to catch even one. 

In fact, the largest known population of Delta smelt doesn’t live in the Delta at all. They live, instead, just south of the watershed, in large white circular lab tanks Hung oversees at the FCCL, now rearing  a captive population in the tens of thousands.

This decades-long effort has been meticulous. The smelt was listed as threatened in 1993 but the project to culture the fish was established only a decade later, in 2004. Since then, FCCL scientists each year scour the estuary in search of wild smelt. Each such specimen found is then transported into the lab to be tagged and genetically cataloged. 

The careful genetic classification of each wild Delta smelt has been key to preserving the genetic diversity of the captive population to keep it as similar to the wild stock as possible. For years, when breeding season comes along, this genetic catalog is carefully consulted to pair-up smelt for mating new generations in the lab. But keeping this cultured population diverse has become harder over the past decade as finding wild smelt has become rarer in the estuary. 

The hard reality: In 2021, California’s Department of Fish and Wildlife’s Fall Midwater Trawl Survey found none at all, prompting scientists to do something they have been putting off for years – begin preparing for the first release of cultivated smelt into the wild.

A long troubling history, and now comes climate change

The Delta smelt raised in captivity do not smell much like cucumbers. Hung mentions that this trait seems to be connected to stress. The smelt at the FCCL have no predators, perfectly saline water, and plenty of food piped into their tanks. Their lives in the Delta are much less comfy.

Importantly, the Delta smelt evolved specifically in, and is named after, the ecosystem of the San Francisco Bay Delta, for thousands of years having an estuary with cool, freshwater running through its many channels. The watershed in modern times feels very different: According to scientist Peter Moyle, associate director of the Center for Watershed Sciences at UC Davis, “that [original] habitat just isn’t there.”

Irrevocable changes in the smelt’s ecosystem began in the 1800s. Non-native species – like the bluegill and largemouth bass – were introduced to the watershed for sportfishing. Fish very similar to the Delta smelt, like the silverside and wakasagi, were introduced soon after as supplemental food for these new game fish. The former meant more predation for the Delta smelt, the latter meant more competition. 

In addition to these new fish in the Delta, regional water programs like the Central Valley Project and the State Water Project began operating in the 1960s. These projects diverted water flows in the estuary to serve communities in Northern California and, consequently, turned the watershed more saline than brackish.

All of this, coupled with rising temperatures and consistently historic droughts in the region, have created a deadly Delta for the smelt; though this is also a reality for many estuaries, worldwide. “Climate change,” said Moyle, “has just accelerated things.”

The Delta smelt has a lifespan of only one year, and its population was initially devastated by a prolonged drought in the 80s. This time, however, recovery proved particularly difficult because conditions continued to worsen and some non-native species adapted to these changes better than the smelt. In past droughts, smelt populations have diminished even as populations of introduced silversides increased.

“We use the term regime shift,” said Brian Schreier, a scientist with the Department of Water Resources (DWR) in West Sacramento, about the smelt’s decline. And this regime shift was not so easy to reverse. Even as the conditions in the estuary worsened, millions of people still relied on these water projects to survive.

Steps leading to boosting number of smelt in the wild

In 2008, the US Fish & Wildlife Service (USFWS) issued a Biological Opinion (BiOp) that expanding the export of water from the Delta would severely impact the smelt population. That action mandated that measures, like reduced pumping, be taken to prevent such a future for the fish. That 2008 BiOp was reversed in 2019, however, when the Trump administration issued a new statement claiming that the smelt population would be fine given that the FCCL has spent decades rearing a robust captive population to supplement the wild fish.

Even though the FCCL’s plan has always been to eventually release these fish into the wild, scientists have resisted doing so for nearly 20 years. They expressed concerns that the captive population might not be fit for conditions in the wild, or that they would adversely impact the wild smelt population that is surviving.

Water and Power Law Group’s Natural Resource Counsel, Paul Kibel, recalls the way hatcheries failed at replacing salmon populations in a 2020 article “Salmon Lessons for the Delta Smelt.” “The replacement assumption has proven faulty,”  Kibel wrote, “as the total abundance of salmon declined at the same time the propagation and release of hatchery salmon has expanded.” In the case of the salmon, the replacement population not only increased competition for their wild counterparts, but they had also been domesticated in the hatchery and were unfit to survive in the wild. 

These were real concerns also for scientists working with the smelt. And though the 2019 BiOp placed excessive and perhaps unreasonable emphasis on the hatchery fish solution, it may have also – temporarily, at least – saved the Delta smelt.

“That was the first regulatory document that actually had legal backing,” said Schreier, “and effectively mandated that supplementation would occur.” And, late last year, for the first time ever, supplementation finally did.

‘A roller coaster’ as 12,000 hatchery smelts were reintroduced

December 15, 2021, marked the first release of hatchery Delta smelt into the wild. More than 12,000 of these fish were transported from their cool, roomy tanks in the FCCL and placed into several barrels in the back of a pick-up truck. They were then driven to Rio Vista where the barrels were transported to a boat and sailed into the channels of the Delta, where the fish were finally released together. 

The road to this release was “a roller coaster,” according to Schreier: It involved many months of experimental trial releases where select populations of hatchery fish were exposed to conditions of the Delta in aluminum cages specially designed to prevent their escaping even as  food and fresh water flowed through. 

“We started under what we thought would be the best conditions,” said Melinda Baerwald, an ecologist at the DWR, about the caged trials. “To be perfectly honest, we didn’t have high hopes.” But she says she was pleasantly surprised when this first trial had a nearly 100% survival rate of the captive smelt.

The research team then tried exposing the hatchery population to progressively worsening conditions to see how they would fare, another step that  proved reassuring. Baerwald recalls one of the last caged trials they did last summer. “It was fairly shocking,” she said.

The team took the smelt out to the Yolo Bypass in the middle of a heat wave. They weren’t expecting the smelt to stay alive for about a week. “But the fish kept surviving,” she said.

74 wild smelt is more than zero … but ‘a desperation measure’?

Since the first release in December, four more releases have occurred in two additional locations. And, since these releases have taken place, local trawling surveys have picked up 74 smelt, compared to the previous number of  consistently zero.

Baerwald and Schreier wanted these releases to take place in the wintertime to ensure the best chances of survival in the increasingly warming Delta. They also mentioned that doing the releases during cooler months allows the captive Delta smelt to spawn the next generation directly in the rivers so they can begin their lives in the watershed.

The scientists are hopeful, but Moyle says  it’s also “a desperation measure.” The factors that caused the wild smelt’s original decline have still not been properly addressed and the smelt are facing increasingly dire conditions. California and much of the U.S. West,  has also been in a drought since February 2020  and the beginning of 2022 continues to be historically dry.

One may wonder what hope there is, really, for such a little fish as the Delta smelt. Human combustion and emissions of fossil fuels continue to cause unprecedented warming around the world. And these hotter temperatures have also been noted to increase drought severity. So long as temperatures continue to rise as predicted, the Delta of today – plagued with unrelenting droughts and contested water projects and chemical runoff – will never be the Delta of the smelt’s past.

And eventually, without a proper habitat to enter into, those hatchery fish will have nowhere to go to.

Hanisha Harjani is a reporter, artist, and student, currently attending UC Berkeley Graduate School of Journalism.