The Delta Smelt: Keystone Species, Political Flashpoint, Possibly Already Extinct

An explanatory series focusing on one of the most complex issues facing California: water sharing. And at its core is the Sacramento-San Joaquin Bay Delta. Stay with kcet.org/baydelta for all the project's stories.

If you've paid attention to California water politics at any point over the last three decades, you've probably heard of the Delta smelt. A tiny, silvery fish about two inches long at maturity, the smelt is uniquely sensitive to changes in California's Bay and Delta... and may already be extinct as a result of those changes.

The smelt inhabits the boundary between fresh and salt water in the Delta, where ocean tides that bring saltwater into the estuary from the Pacific Ocean meet freshwater flows from California's rivers. Though its historic range encompassed, at different times, the entire Delta and parts of Suisun Bay, our diversion of that freshwater for our own uses has changed the smelt's habitat.

As a result, the smelt has suffered badly. In 1993, it gained protection as a Threatened species under the the U.S. Endangered Species Act, and that listing has played a role in some of the most contentious political rhetoric in modern California. But the controversy hasn't sustained the fish. Far from it: surveys earlier this year turned up a total of six smelts, and biologists warn the fish will likely be extinct in a few years -- if it isn't already.

The smelt, Hypomesus transpacificus, was historically found in low-salinity water where freshwater and brackish intermixed. That mixing zone was rarely static in the pre-development Delta, shifting toward San Francisco Bay during times of heavy spring runoff and inland during fall, or during drought periods.

The smelt shifted positions within that mixing zone as well, seeking out depths that better matched its preferred salt concentrations, or moving into fresher water in the Delta's upstream tributary side channels in order to spawn.

In that sense, the smelt could almost be seen as an anadromous fish like the Chinook salmon that whizzed past it on their way to the open ocean or headwaters spawning grounds: both hung out in saltier water but headed for freshwater to reproduce. But the smelt never got all the way into undiluted seawater. The saltiest water in which Delta smelts have been found has a salinity of about 14 parts dissolved salt per thousand parts water. In general, the smelts seem to prefer water that's around 2 parts per thousand. Seawater runs about 35 parts per thousand.

If you're having trouble picturing what that means, look at it this way: to make water that smelts feel comfortable in, put 17 and a half gallons of fresh water in a tank and then add a gallon of seawater. If you add six more gallons of seawater to the tank, you'll make the water salty enough that the smelt will really wish they were somewhere else.

And that's pretty much what's happened to the smelt's habitat. Our statewide thirst for fresh Northern California water has meant more water goes into canals and aqueducts, and less flows out through the Delta to San Francisco Bay. That lower freshwater flow means that the tides carrying salt water into the Delta meet less resistance on their way inland, which means saltwater intrudes deeper into the Delta, driving salinities way past the level Delta smelt can live with, and making that optimal salinity "mixing zone" a lot smaller.

The giant pumps we use to divert much of that water take a direct toll, through what's called "entrainment," a slightly more palatable way of saying the fish get mortally injured when they're sucked into the machinery.

And even if the smelt never reach the pumps, confining them to a much narrower area by constricting that mixing zone brings the smelt into increased contact with other fish, most of which are perfectly happy to swallow a tiny two-inch fish. The fact that about two dozen dams now trap all the sediment that used to flow into the delta each spring, giving the smelts a bit of cover in the murky water, hasn't helped either. In summer and fall especially, the Delta water clears up, exposing any remaining smelts to predation from fish and other hunters.

Lastly, pollution from sources upstream, such as Sacramento Valley cities, may also be a significant threat to the Delta smelt. Nitrogen compounds from fertilizer runoff and malfunctioning sewage treatment plants seem to be the biggest such problem. Those compounds break down into ammonia, among other compounds: ammonia reacts with the Delta's slightly acidic water to form the ammonium ion. High concentrations of ammonium ions in Delta water have been shown to reduce reproductive success in many fish, the smelt included.

Less than a century ago the Delta smelt was one of the most abundant fish in the Bay and Delta. Found in large schools throughout the Delta from Sacramento to Manteca, and as far west as Suisun Bay, there were enough Delta smelts in the estuary to support a commercial fishery until the mid-20th Century.

If we'd been able to keep that fishery going without doing the species in, the Delta smelt would have been an excellent sustainable seafood species. It was near the bottom of the estuary's food chain, the larvae and adults both subsisting on plankton animals such as copepods. Unlike long-lived ocean-going species such as the critically overfished swordfish, Delta smelts mainly live for just a year. About a tenth of the typical smelt population survived into a second year. That would have meant that if a few too many tons of smelt got taken in a particular year, a couple restricted seasons could have allowed the fishery to recover, as new smelt smolts tumbled downstream into the mixing zone and gobbled the plankton caught in the zone's turbid currents.

And the smelt's distinctive cucumber aroma when fresh might have added an interesting dimension to local sushi.

But there are no more "tons of Delta smelt" remaining in the Delta. At this point, the fish is only a little more abundant than unicorn tears. The last five years of drought may well have been the icing on extinction's cake for the smelt. In March of this year, an annual survey of smelt numbers conducted by fisheries biologists working with the California Department of Fish and Wildlife counted just six smelt. That was down from an already startlingly low 88 in March 2014, and hundreds in previous spring surveys.

That low count prompted smelt expert and veteran California fisheries biologist Peter Moyle of UC Davis to offer a bleak forecast to National Geographic's Jane Kay. In April, Moyle told Kay that he expected the smelt had little chance of surviving.

"The probability of the delta smelt surviving in the next three years is relatively low. The chances of its bouncing back from where it is today seem very unlikely," said Moyle. "There are a lot of things going on simultaneously. Everything that stresses that poor fish is out there. The drought is the final straw."

What the six fish found in March's sample means about actual numbers of remaining Delta smelt is a matter of dispute. It's exceedingly unlikely that the count got every last smelt in existence, after all, the difference between counted numbers and actual numbers has been a matter of some dispute in the last decade. That happened most notably when a federal court judge cited uncertainty of the smelt's numbers, and how many of the smelt are actually getting "entrained" in Delta pumps, when he ordered the U.S. Fish and Wildlife Service to rewrite its 2008 Biological Opinion on whether continued operation of the State Water Project and Central Valley Project would hurt the Threatened fish.

As I wrote in March, 2014, that was just one decision in a hugely complex series of documents, lawsuits, court orders and further documents that's still in progress to this day.

If only we could be certain that Delta smelts were as plenteous as the court filings and legal documents that concern them.