Salinity may be greatest threat to dwindling Delta smelt, engineers find

A new analysis by engineers at the Contra Costa Water District shows that a decision made a decade ago to protect fish by shifting the timing of water deliveries could be at the root of what is causing populations of Delta smelt and other fish to crash.

The engineers found that the shift led to saltier water in the fall, and for some reason, that is leading to fewer fish.

The evidence appears to be the strongest explanation yet for an environmental crisis in the Sacramento-San Joaquin Delta that threatens not only the survival of at least one fish species but also the reliability of water supplies from the Bay Area to Southern California.

And although it is only now that rising salinity is emerging as a possible key to the mysterious decline of Delta fish, data supporting that theory have been available for decades, meaning the decline of Delta smelt and other species could have been predicted -- and addressed - earlier.

"Quite frankly, these are the kinds of analyses that should have been done 10 years ago," said Tina Swanson, a senior scientist at the Bay Institute, an environmental research group.

The water district's work suggests responsibility for the Delta's health could be distributed more broadly than is commonly assumed because salinity levels are affected by all users of the water that flows into the Delta and not just those who pump out of the Delta.

The Delta, the West Coast's largest estuary, is a complex ecosystem influenced by the tides rolling in from the ocean and the flow of snowmelt from the Sierra Nevada. Balancing the flow of water into the Delta with the amount of water pumped out is a tricky business and one not always well understood.

A decision made a decade ago to protect Delta fish by shifting water shipments to the San Joaquin Valley and Southern California from the spring to other times of the year, for example, could be contributing to the unprecedented environmental crisis.

The shift protected fish that spawn near the intakes of giant water pumps at Tracy and the juvenile salmon that migrate past them on their way to the sea. But it had an unintended consequence of making the Delta saltier in the fall.

The higher salinity may have helped the spread of an invasive clam that was just gaining a foothold in the estuary during the 1990s.

And that could be what is causing Delta smelt and possibly other fish species to decline sharply, according to an emerging scenario developed by the Contra Costa Water District.

The clams, which arrived by ship from Asia around 1986, now carpet much of Suisun Bay and consume prodigious amounts of plankton and other food that small fish need to survive.

They appear to be undercutting the food web in Suisun Bay and the western Delta, key habitat for longfin smelt, striped bass and young Delta smelt, often considered an indicator of the health of the Delta.

Nothing has been proven, and the analysis has so far focused only on Delta smelt, but the broad outline of what might be driving the collapse of several fish species is emerging from different directions. Working from the top down, engineers at the Contra Costa Water District crunched numbers and found a remarkably close relationship between fall salinity and the population of Delta smelt, a tiny fish found nowhere else.

Scientists, meanwhile, are working from the bottom up, tweaking and testing theories in an effort to understand why the Delta smelt and other fish species are declining.

That work, done by a team of scientists called the POD, for pelagic organism decline, is building toward some of the same conclusions that the Contra Costa Water District engineers found.

"I think where Contra Costa is going is the same place the POD team is going," said Bruce Herbold, a biologist at the U.S. Environmental Protection Agency. "I think the POD team is much more methodical in their approach. I expect as time goes by, I think we'll converge more."

Last year, state fisheries biologists looked at the numbers of fish caught in recent years during annual surveys and discovered the populations of several species of fish were declining rapidly for no discernible reason.

Fish populations in the Delta regularly bounce up and down, but this time, many species were declining simultaneously, and there was nothing about the weather or the water flow that could explain it.

The crash appeared to have begun around 2001 or 2002 and affected the major "pelagic," or open water species, including Delta smelt, longfin smelt, threadfin shad and striped bass.

Strangely, it was only the young of the striped bass that were affected. Once stripers reach a certain age, they appear to do fine.

For Delta smelt, the most imperiled of the fish species, the slide worsened markedly last year and raised concern among some environmentalists that it finally could be heading for extinction after a 20 year decline.

Scientists last year said the cause of the population declines could likely be traced to three broad categories.

Water "exports" from the massive pumps that provide irrigation to much of the San Joaquin Valley and drinking water to 23 million Californians were one possible cause. Toxic substances, including the pesticides in farm and city runoff, were another. Invasive species, including clams that might be eating food sources of native fish, were a third.

Today, none of those three has been eliminated, and many experts say a combination of all three is at play.

"Exports are part of the problem, but I don't think much more than any other diversion that's affecting salinity," said Greg Gartrell, the assistant general manager of the Contra Costa Water District who oversaw the analyses. "It's clearly pointing the finger at the clams, but it doesn't rule out toxics or pesticides."

The Contra Costa Water District's work presents a strong statistical case that the salinity of the Delta in the fall determines the Delta smelt's population the following year.

The results not only establish that salinity and Delta smelt trends are related, they show that by knowing the salinity of the Delta in the fall, the following year's smelt population can be predicted accurately.

How salinity determines the fate of Delta smelt remains a mystery, but the link could be the overbite clam, which gets its name from its mismatched shell halves and thrives in brackish water.

The district's model takes the fall smelt population and salinity of the Delta in the fall and predicts the following summer's smelt population. The model is accurate for the years since the late 1980s, shortly after the clam arrived. But the relationship breaks down entirely in the years before the clams' arrival.

"This doesn't eliminate exports as a cause. This doesn't eliminate toxins as a cause. But it does point a big finger at the clams as a possibility," said Gartrell.

The data used by his staff were available to scientists and water officials for years, but no one analyzed them adequately, he said.

"The mistake of not looking carefully at what is available cannot be repeated," he said. "This decline could have been seen in advance, regardless of what the causal link is."

One reason is a full scientific investigation, which could explain exactly what is happening and why, is still pending.

Although the pumps delivering water to Southern California do affect water quality, they are no more at fault than other water users when looking at the big picture, said Gartrell.

The East Bay Municipal Utility District, which has dams on the Mokelumne River, and the San Francisco Public Utility District, which dams the Tuolumne River, do not pump water out of the Delta. Nevertheless, their upstream activities influence Delta salinity by decreasing the flow of fresh water into the Delta.

The effect of higher salinity might also create problems beyond causing clams to spread. It could be forcing the fish upstream to lower salinity zones, where they might be more vulnerable to being sucked into pumps, or more exposed to agricultural drainage.

If the water district is correct, one obvious response might be to increase fresh water flows into the Delta in the fall. But it is not known how well that would work or how much water would be needed.

This year, for example, making the Delta fresher would be relatively easy because the higher-than-average rainfall has eased the supply crunch. But in dry years, restricting the outflow could be very costly to some water users.

And increased fresh-water flows would not solve the problem in a year. The clams would start creeping back upstream as soon as salinity rises again.

"It's possible that fall salinity is affected by outflows that are not manageable," said B.J. Miller, a consultant to water users in the San Joaquin Valley. "It's not water project operations. It's the weather."

Miller, like Gartrell's team, has crunched numbers to show that Delta smelt populations are determined by whether fish and the zooplankton they eat are in the same place during the summer. Using that information, Miller can predict Delta smelt populations in the fall.

But fine-tuning when and how much water gets pumped out of the Delta could be skirting around the fundamental issue. It could be that the Delta is no longer capable of delivering as much water as is demanded of it.

"Maybe we've exceeded the capacity of the system. That's one thing people should be thinking about," said Swanson of the Bay Institute.

"We are delivering more water than we ever have before," said Herbold. "I think if we're going to have an aquatic ecosystem that isn't just a water delivery system, we're pushing the limit."

One prospect for crafting a solution is a "habitat conservation plan" that state water officials could use to protect threatened and endangered species such as the Delta smelt and generate money for environmental improvements.

Joe Grindstaff, who is leading the effort as director of the California Bay-Delta Authority, said the Contra Costa Water District's findings could prove to be a stick that encourages more agencies to participate.

That is because anyone who causes salinity to rise could be required to address its impact under the Endangered Species Act.

For example, the East Bay Municipal Utility District and the San Francisco Public Utility District so far have been merely "observers" of the habitat conservation plan. That could change, Grindstaff said.

"Neither one has agreed to participate," he said. "If Greg (Gartrell at CCWD) is right, they might well be."

So....environmentalist-scientists alter water releases to "help" one breed of fish;thereby hurting all fish.

That is the current position that could change again in 10 years.

The original flows into the Delta before our system of water storages was built were less than we send into the Delta now.I don't know how they can surmise low flows in the Fall are doing the damage.

Michael Crichton has written extensively about the fact that we don't really know HOW to "protect the environment."

Just about all environmental activism assumes that the appropriate action is perfectly well understood and all we need to save the environment is the will to implement it.

Unfortunately, the world is a complex place. The Law of Unintended Consequences never sleeps. A lot more humility is appropriate for environmentalists.

If we want to protect wilderness, for instance, we first have to figure out HOW to do it.

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