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Little Fish in Big Trouble: The Bay Delta's Longfin Smelt

Alviso Slough near san Jose, where longfin smelt are enjoying more than the usual amount of fresh water. | Photo: Sathish J. some rights reserved
Alviso Slough near San Jose, where longfin smelt are responding to extra fresh water by having babies. | Photo: Sathish J., some rights reserved

Heavy rain brought relief to the people, plants and animals of California this past winter. The earth is soggy, farmers are looking at plentiful summer irrigation supplies, and rivers are full and flowing.

The recent rains also may have given the longfin smelt a reprieve from extinction… at least for a while.

The longfin smelt, Spirinchus thaleichthys, is among the many natives to the San Francisco Bay-Delta ecosystem that have been edging closer and closer to the brink of oblivion each year for a decade or two. The longfin is less famous, and a bit less imperiled, than its cousin the Delta smelt—that little fish that has unwittingly become a loaded political symbol in the fight over river water between farmers and environmentalists.

And while the Delta smelt is now about as close to being extinct as an extant species can be, something extraordinary happened this past winter for the longfin smelt: The fish successfully spawned in the southern reaches of San Francisco Bay, where scientists recently found larval-stage longfin smelt in sampling nets for the first time.

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“Every year, we’ve seen adult longfin smelt overwintering in the area,” says James Hobbs, a research scientist at the University of California at Davis who has been studying smelt in the South Bay since 2010. “But this is the first time in seven years that we’ve seen recruits from the spawning.”

It probably has something to do with the rain. Longfin smelt, which venture into open ocean waters at times, will only spawn in water that is anywhere from drinkably fresh to 8 or 9 parts per thousand of salinity—about one fourth the salinity of most ocean water. Most years, they must swim upstream toward the Sacramento-San Joaquin Delta region to find conditions suitable for spawning.

“But in these extreme wet winters, they’re able to use much more of the entire estuary because salinity drops so much,” he says.

James Hobbs | Photo: James Hobbs, via LinkedIn
James Hobbs | Photo: James Hobbs, via LinkedIn

Hobbs says that in early 1983, during a particularly wet El Niño-influenced winter, scientists with the Department of Fish and Game (now Wildlife) saw evidence that the longfin smelt was spawning in the South Bay near San Jose. This, combined with the 2017 observations, reinforces what many biologists have known all along: Fishes native to San Francisco Bay thrive when the estuary receives plentiful wintertime supplies of freshwater. In fact, while longfin smelt numbers have been declining for years, annual population surveys usually show a dramatic abundance spike immediately after exceptionally wet winters. This happened in 1998, in 2006 and in 2011.

It’s obvious: These fish need fresh water. So do striped bass, salmon and sturgeon. So does the Delta smelt — and because this tiny fish is economically worthless and relatively uncharismatic, the agriculture industry has singled it out as their hated whipping boy. That is, when environmental laws call for a temporary reduction in pumping of water from the Delta, farmers and their lobbyists often blame it on the Delta smelt.

They do this even when other environmental factors — like keeping salty Bay water from intruding into the Delta or allowing young salmon to swim uninterrupted to the ocean — have prompted the pumping reductions. When the Delta smelt goes extinct (a near certainty at this point, depending on how you define “extinct”), these users just might find themselves looking for a new scapegoat to blame for their grievances during drought years — and the longfin smelt could be the obvious next candidate, assuming it isn’t also extinct.

There have probably never been fewer longfin smelt than there are now. The longfin was once one of the most commonly found fishes in San Francisco Bay. There was even a cannery in the Suisun Marsh that processed heaps of the smelt. In the 1960s, when the Department of Fish and Game began conducting their annual trawl net population surveys in the Bay and Delta, longfin smelt essentially clogged their gear. Biologists caught more than 80,000 longfin smelt in their first survey, in 1967. Even into the early 1980s, the longfin smelt remained one of the most abundant forage species in the bay.

Longfin smelt (bottom) compared to the better-known Delta smelt (top) | Photo: Randall Baxter/California Department of Fish and Wildlife
Longfin smelt (bottom) compared to the better-known Delta smelt (top) | Photo: Randall Baxter/California Department of Fish and Wildlife

“They were a really important food source for birds,” Hobbs says.

But starting about 15 years ago, numbers of virtually every native fish species routinely caught in the annual samplings began to plunge — a phenomenon local scientists call the “POD,” or pelagic organism decline. The synchronous crash of so many species indicates an ecosystem implosion. While longfin smelt, of which biologists counted just seven in their 2016 survey, can be affected negatively by poor ocean productivity, independent researchers agree that the problems are mostly upstream.

Water diversions are the simplest, if not the only, problem to identify. In the 1960s, federal water pumps were removing about 1.5 million acre-feet of water per year from the Delta. After the installation of the State Water Project’s pumps late in the 1960s, water diversions increased steadily. By the late 1970s, the pumps were drawing 4.5 million acre-feet each year. By the early 2000s, diversions exceeded 6 million acre-feet annually. Salmon runs in the Sacramento crashed to historic lows several years later. By this time, populations of all the native fishes, as well as nonnative but naturalized striped bass, were plunging, with bar graphs showing abundance indices of the species flattening out to near zero. The ecosystem was in full collapse. 

Compared to the longfin, the Delta smelt is a relatively easy fish to understand. It lives for just one year and spends that entire time in the Delta region. This makes it a perfect canary in a coalmine, and the near disappearance of the fish indicates there is the native habitat and ecological balance of the Delta is seriously out of whack.

With the longfin smelt, things are not so simple. The fish lives for several years, spawns in freshwater and ranges many miles out the Golden Gate into the ocean. This makes it very difficult to pinpoint just what is ailing the species. Hobbs says he hopes he and his colleagues discover a “secret, silver bullet”—a remedy that could save the many Delta-based species now looking extinction in the face.

Early juvenile longfin smelts | Photo: USFWS
Early juvenile longfin smelts | Photo: USFWS

The trouble is, there are many factors affecting the ecosystem these fishes live in, not just a simple shortage of water. Agricultural lobbyists know this and are now using the complexity of the situation to deflect attention away from the Delta pumps. For instance, they often say that water pumping restrictions have been impacting their livelihoods for more than two decades, and still the Bay and Delta’s fishes are vanishing. Thus, their argument goes, we must begin to identify other more effective solutions than just reducing water diversions.

Most scientists generally feel that removing vast volumes of water from the Bay Delta ecosystem plays a significant role in degrading habitat and reducing fish numbers. But the agricultural lobby is correct to some degree: There is a lot wrong with the Bay Delta ecosystem, and whether or not San Joaquin Valley farmers will agree that irrigating orchards with water from the Sacramento River has anything to do with fish declines, there are certainly other conditions and human activities that must be addressed. For instance, the release of warm water from dams at the wrong time kills salmon. Invasive clams, which filter nutrients from the water, are outcompeting native fishes for food.

"The energy that once circulated through the food chain has accumulated in these clams," U.C. Davis fishery biologist Peter Moyle explained to me in an interview several years ago.

Smelts of the Bay Delta

Even far downstream in San Francisco Bay, the longfin smelt is affected by alterations to the banks of the Sacramento River, Hobbs says. Here, the clearing of riparian brush and trees has exposed shallow waters to direct sun exposure. This warms the water to levels the longfin smelt cannot tolerate.

“These fish are so sensitive to temperature, and they’re already at the upper end of what they can tolerate,” he says. “Any more warming is going to be the end of them.”    

Hobbs grew up in Antioch and spent much of his youth getting wet and muddy in the Delta. He would often fish from the pier at the Pittsburg marina for small fish, which he and friends then pinned onto larger hooks and used to catch striped bass. Those little fish, he speculates now, were “likely smelt.”

As a local with roots set deep in the waterways of the Delta, Hobbs finds the collapse of the San Francisco Bay estuary very personally troubling.

“It affects my psyche deeply,” he says. “It’s what keeps me working so hard. It’s such a dire situation.”

Hobbs’ research team found adult longfin smelt packed with ripe gonads in the South Bay late last year. The capture of larval stage smelt a few weeks later is essentially proof the that the fish spawned in the area.

Take a good look: despite this favorable year, the longfin smelt may not be around much longer. | Photo: U.S. Bureau of Reclamation
Take a good look: despite this favorable year, the longfin smelt may not be around much longer. | Photo: U.S. Bureau of Reclamation

Specifically, the fish seemed to be spawning in the restored Alviso Marsh, inside what once was a salt pond. The breeding location is also, incidentally, very near where 100 million gallons of treated wastewater enters the Bay every single day. This was stirring news for the city officials who heard about the smelt spawn, since it indicated the San José-Santa Clara Regional Wastewater Facility was working well.

“We were really excited to learn that longfin smelt were spawning in the waters surrounding the Regional Wastewater Facility,” says Kerrie Romanow, director of the Environmental Services Department. “The former Alviso salt ponds support an amazing array of wildlife, from peregrine falcons to anchovies. We are proud to play a part in supporting this diverse and vital habitat.”

But the longfin smelt remains in big trouble, for the population effects of a good spawning year will only go so far.

“These fish only live for two or three years, so a great spawn doesn’t last long in the population,” Hobbs says. “That’s the problem with these small bait fish. You need successive years with good conditions.”