Thursday, Sept. 20, 2007 | ON THE SACRAMENTO-SAN JOAQUIN RIVER DELTA — Two men in a fishing boat slide through the glassy, slate-green water here, throwing hopeful casts in search of trophy bass.

Jeffrey Mount, a tan, energetic geology professor from University of California, Davis, gestures at the fishermen, who are trolling around the grassy remains of an earthen levee that collapsed more than 70 years ago. More than 140 levees have crumbled in the last century and flooded thousands of acres, Mount says, and more will continue breaking and causing devastating floods.

“All signs point to that as the future of the delta,” the professor says, from the deck of a touring catamaran. “It’ll be a good place to have a boat.”

The Sacramento-San Joaquin River Delta sits 450 miles north of San Diego — far enough away that it can seem like little more than a notion, a foreign place. But the delta’s 738,000 acres of crops, riverfront housing and heron-lined waterways are very real and vitally important to San Diego’s drinking water supply.

When the winter snows blanketing the Sierra Nevada melt, the runoff cascades into rivers that flow west toward San Francisco Bay, beneath the Golden Gate and out to the Pacific Ocean. If that snowmelt were a train, the delta would be its tracks.

But the delta, which is one-fourth the size of San Diego County, is under duress. Both its ecosystem and its infrastructure hover on the brink of collapse, from the smallest fish to the largest levee. A 6.5-magnitude earthquake would be strong enough to rattle miles of soft, earthen levees — little more than unstable mounds of peat — into a substance the consistency of toothpaste.

Trouble in a far-off estuary might not be concerning, except that San Diego County gets as much as 70 percent of its water from the delta, a triangle-shaped area bounded by Sacramento, Tracy and Antioch and home to 515,000 people. A major earthquake could shut off that spigot for years.

Attention has turned to the delta this summer, however, because of the threat posed by manmade problems — not the natural kind. The population of the delta smelt, a three-inch-long fish listed as threatened under the federal Endangered Species Act, has dropped to its lowest recorded levels. The tiny fish, considered a bellwether of the delta’s ecological health, sits on the verge of extinction.

Invasive species have reduced the fish’s major food source. And massive pumps that draw water out of the delta and send it to Southern California have chewed up thousands of the smelt. The two forces have combined to wreak havoc on the delta smelt.

“It’s like Murder on the Orient Express,” says Bruce Herbold, a U.S. Environmental Protection Agency biologist. “Everyone did it. Everyone’s guilty.”

To help protect the fish, Fresno-based U.S. District Judge Oliver Wanger ordered a decrease in the amount of water pulled out of the delta next year. The goal: To reduce pumping when the fish are likely to be nearby. The ruling could cut the amount of water exported from the delta by 37 percent. Some San Diego farmers will begin seeing cutbacks in January. Unless a wet winter comes to the Southwest, which has been mired in drought, more severe restrictions could follow.

The judge’s order is temporary, and the future of the delta is uncertain. Billions have been invested in its infrastructure. To understand why billions more will be spent in coming years, you have to understand the complexity and breadth of the problems that afflict the smelt, the delta and your water supply.

Savior or Killer?

Standing inside a fluorescently lit warehouse, a man with a diamond-studded ring and matching tie clip makes a bold pronouncement.

“We don’t kill fish,” Michael Miller says loudly. “We save them.”

A few feet away, in a holding tank filled with swirling water, a dead fish floats belly-up, its pale body spinning in clockwise circles, around and around.

Miller is a tour guide for the state Department of Water Resources, the agency responsible for operating the pumps that push water out of the delta over a mountain and into an aqueduct where it’s destined for 750,000 acres of agriculture and 23 million faucets.

No habitat exists downstream of the pumps, just a 444-mile-long cement channel and a reservoir that satiates Southern California’s thirst. So the state attempts to screen out marine life, with limited success. Billions of gallons of water pass through the Skinner Fish Protective Facility each day. Inside that warehouse, a 24-hour crew regularly hauls up a net to see what marine life they’ve sucked in. They index their catch and truck the fish upstream and dump them back out into the delta.

On a recent morning, a man with a ballcap and a Fu Manchu pawed through a haul to record every trapped fish. Each got two numbers.

“One, 42,” the man says. “Six, 20.”

The first identified the fish. On this day, that meant the pumps were pulling in American shad and threadfin shad. The second was its length in centimeters. Most small fish were barely as long as a Matchbox car — just a spine, two googly eyes and a translucent body. The process was imperfect. The man dropped some fish on the floor, where they writhed against the wet cement. He would scoop them up and toss them into the next holding tank, where that dead white fish spun in endless circles.

Around this facility, the delta smelt is bad news. In May, the smelt began showing up in those routine counts. That’s a sign the smelt were hanging around near the pumps. The weak swimmers aren’t strong enough to escape the pumps’ pull. The stress of the screening process complicates the problem, increasing the likelihood that a fish — even one that has been kept out of the pumps — will die.

At the same time the smelt appeared at the screening facility, biologists trawling for the smelt elsewhere in the delta found precipitous drops in its population. Survey nets that had previously raked in almost 3,000 smelt pulled in only a few dozen.

So for nine days, the state turned off the pumps. It is a precursor of what the federal judge ordered next year.

The pump’s effects are “very subtle,” says Bill Bennett, a research ecologist at the Center for Watershed Sciences at UC Davis. The problem isn’t how many fish the pumps kill, but which fish the pumps kill.

“The pumps have been acting against natural selection,” Bennett says. “They’re taking some delta smelt that apparently are very necessary for the population to survive critical periods. They’re taking some of the robust individuals on a regular basis.”

By summer, when the weaker smelt migrate to the delta’s western fringes, they settle in an area that doesn’t have as much food as it once did — another subtle impact.

For that, researchers blame a bivalve known scientifically as Corbula amurensis.

The overbite clam.

The Clam Invasion

It’s easy to picture: A hulking freighter, steaming across the Pacific Ocean with a belly full of cargo and, out of sight somewhere below deck, a foreign invader lurking in the shadows.

It was 1986. A ship packed with Nissans journeyed into San Francisco Bay with tanks full of ballast water from an Asian port. The water would have kept the ship stable during its cross-ocean voyage. Somewhere in the brine was a small clam with a funny-looking overbite. One half of its white shell was slightly larger than the other.

When the freighter dumped its ballast in the bay — scientists have been able to trace the incident to the exact ship, a rarity — the clam went with it. A community college professor discovered the bottle cap-sized clam during a routine voyage to sample the bay’s water quality.

Each year, hundreds of species find their way into San Francisco Bay this way. But few survive in their new habitat. The overbite clam was different. Its population exploded. Researchers still tell stories about sampling the bay’s muddy bottom and being shocked when they pulled up thousands of clams that hadn’t lived there a few years earlier. As the late 1980s faded into the 1990s, the clam continued thriving, pushing further inland. Toward the delta smelt’s habitat.

The clam’s move inland underscores the reason that scientists are often concerned about the introduction of nonnative species. New organisms can tip the balance of sensitive ecosystems. The clam started feasting on phytoplankton, the basic building block of the food chain. That meant less food for zooplankton, the next building block and a mainstay of the delta smelt’s diet.

Other fish have been affected by the pumps and the clam, too. Since 2001, the delta’s populations of threadfin shad and striped bass also declined precipitously, says Bruce Herbold, the EPA biologist. But the delta smelt is unique. It’s the only declining fish found exclusively in the delta. The longfin smelt, which has been proposed for listing under the Endangered Species Act, lives longer and has a more widely distributed population, found as far north as Seattle.

But for the delta smelt, the Sacramento-San Joaquin River Delta is its only home. For better or worse, the delta is its aquarium.

And, says Bennett, “it’s a very different aquarium than it was 30 or 40 years ago. [The smelt] are a really good poster child for what the delta system was.”

The Shifting Delta

Before the first miner struck gold, the delta looked nothing like it does today.

Rivers flowed freely. Freshwater tidal marshes covered two-thirds of the land.

Today, 1,100 miles of earthen levees have turned rivers into manmade channels. Farmers’ fields and subdivisions have supplanted the wetlands, capitalizing on the delta’s rich soil.

The transformation started in the mid-1800s. Gold rush fever hit, and Manifest Destiny drew out a generation of Civil War soldiers. Many who didn’t strike it rich turned to agriculture, providing sustenance for burgeoning mining towns.

Gliding on the boat along the sun-drenched Sacramento River, Mount, the UC Davis geology professor, reflects on the region’s evolution from pre-Gold Rush wetlands to turn-of-the-century asparagus hub to today’s vital-but-fragile water source. Soon, Mount predicts another shift. The question is to what.

“This is not a static landscape,” Mount says. “It is constantly evolving. The delta is going to be something different. And we’re in the process of deciding that.”

Friday: As the delta faces crisis, a controversial concept is revived.

Please contact Rob Davis directly with your thoughts, ideas, personal stories or tips. Or send a letter to the editor.

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