By Dale Kasler and Phillip Reese

Their populations dwindling, Northern California's fish suddenly are taking a leading role in the drought-related drama gripping the state. State regulators, alarmed at declining numbers of winter-run Chinook salmon, acted in late May to temporarily curtail the flow of water from Lake Shasta, hoping to cool the giant reservoir's waters and prevent another massive die-off of juvenile fish. The move means less water, at least for the time being, for farmers and urban Californians downstream.

Last week, a group of environmentalists sued state and federal regulators in U.S. District Court in Sacramento, accusing them of giving humans billions of gallons of water that had been earmarked for salmon, Delta smelt and other species that ply the Delta. Those actions have brought several species "to the brink of extinction," the lawsuit says.

The plight of California's fish is not a new element in the state's protracted water wars. Several species have been listed by the government as endangered or threatened for years, bringing legal protections and sparking conflicts with farmers and others over the state's limited water supply. Now the divisions are deepening. As the drought stretches into a fourth punishing year, with California unable to satisfy all competing interests, the demands on behalf of fish are sharpening the battle lines and creating additional headaches for regulators.

California is stuck with "a host of choices between terrible outcomes," said Felicia Marcus, chair of the State Water Resources Control Board, the agency charged with refereeing the fights over water.

Right now, no one's particularly happy with the decisions being made. Cities have been ordered to cut consumption by an average 25 percent; farmers have lost one-third of their normal allotment of surface water pumped in through government canals.

Environmentalists argue that California's fish are suffering worst of all. The state's monthly surveys of the Delta smelt population found just one of the diminutive fish in April and eight in May. Almost all the juvenile winter-run Chinook salmon died last year, suspected casualties of a shortage of cool water in the Sacramento Valley's rivers and streams.

Jon Rosenfield, a conservation biologist at the nonprofit Bay Institute of San Francisco, said the state and federal regulators who govern California's water have erred by diverting supplies away from fish in the past couple of years. The result is that some species are being driven toward extinction to bring short-term relief to farms and cities.

"We have mechanisms for getting people through tough economic times," Rosenfield said. "We have a way of dealing with it that does not involve species going extinct. Our management is leading toward permanent consequences, things that can't be undone."

The declining population of winter-run Chinook creates problems for California's $1.4 billion-a-year salmon fishing industry. Even though commercial fishermen mainly harvest fall-run salmon, whose numbers are healthier, concerns over their winter-run cousins have prompted the U.S. government to place unusual restrictions this season on catches of all Chinook at various points off the California coast.

That creates concerns for commercial fishermen such as Dave Bitts of Eureka, who's been catching salmon for 40 years.

"It's our life's blood, basically," said Bitts, president of the Pacific Coast Federation of Fishermen's Associations.

A legal obligation

Farmers say they want the fish population to thrive, too. But they argue that salmon and smelt aren't suffering because too much water is going to agriculture. Rather, the main culprits are habitat problems and predators such as largemouth bass, said Mike Wade of the California Farm Water Coalition.

Throwing more water at fish isn't doing them any good, Wade said, but it is hurting farmers. He said farmers are particularly upset by the state water board's decision to curb water releases from Shasta in order to protect the winter-run Chinook.

Such a move, undertaken during planting season, "is devastating to agriculture," he said. "There's water in Shasta that farmers throughout California have been depending on. Now the rug has been pulled out from under them."

Steve Evans, a program coordinator at the Friends of the River advocacy group in Sacramento, is among the environmentalists who counter that agriculture is weathering the drought much better than fish. Despite the fallowing of hundreds of thousands of acres, farm employment -- and overall crop revenue -- actually grew in California last year, according to government statistics. Meanwhile, Evans said, the fish continue to lose water.

"There is huge political pressure to take more water from the environment," Evans said. "Every time a legislator writes a letter to the Bureau of Reclamation and complains about his constituents not having enough water, it puts pressure on them." The bureau runs the Central Valley Project, the federal government's massive network for pumping fresh water north to south in California.

The fish are by no means defenseless. In 1993, Congress rewrote the rules governing the Central Valley Project to help the environment. In particular, lawmakers ordered adjustments in the operation of the giant pumps near Tracy that route water to the farms and cities of the San Joaquin Valley and Southern California.

Under the new law, more water is allowed to flow through the Sacramento-San Joaquin Delta, carrying fish to the ocean, instead of being pumped south. That extra flush of water also keeps the Delta's delicate ecosystem in balance by acting as a barrier against ocean salt water.

Long before that, the U.S. government committed itself to protecting species that have been designated endangered or threatened. The Endangered Species Act, passed in 1973, declared that the United States would "conserve to the extent practicable the various species of fish or wildlife and plants facing extinction."

The law packs a punch. In one famous case, in the late 1970s, the U.S. Supreme Court prevented completion of a hydroelectric dam in Tennessee to protect a previously undiscovered fish called the snail darter. Congress eventually passed a law exempting the dam from the species act, but the case was seen as proof that the courts would enforce the law. (The dam did open, and the snail darter was later found in other locations.)

In California just last year, a federal appeals court jumped to the defense of the tiny Delta smelt, which is listed as threatened. The court said the government's pumping mechanisms in the Delta could be shut off to prevent excessive numbers of smelt from being sucked into the pumps and killed. The ruling was a big defeat for farm groups and the Metropolitan Water District of Southern California, which were clamoring for more water to come through the pumps.

"Legally, fish actually have quite a bit of clout," said Peter Moyle, a biologist at UC Davis' Center for Watershed Sciences. "There's a legal obligation to keep fish going."

Such protections are not ironclad, however. In a series of emergency orders in the past year, the state water board allowed several hundred thousand acre-feet of water to be routed away from fish and given to the Central Valley Project and its state counterpart, the State Water Project.

The twin projects encompass the complicated system that delivers water from Northern California, which has 70 percent of the state's water, to the farms and cities of Southern California, which has 70 percent of the population. An acre-foot is nearly 326,000 gallons.

Redirecting the water wasn't done lightly. "Fish populations now are at record low levels and cannot be considered resilient at all," the water board's executive director, Tom Howard, wrote in an April order. But he said he believed the decision "strikes a reasonable balance" between the environment and human demands.

Howard's reasoning did not impress the California Sportfishing Protection Alliance, which led a consortium of environmental groups that sued the water board and other regulatory agencies last week. The groups said the diversions are causing enormous harm to, among others, the winter-run Chinook salmon.

"Every drought, the first cut, the first pain, comes out of the fish," said Bill Jennings, executive director of the sportfishing group.

Unintended consequences

Like the smelt, Chinook salmon are not exactly the prettiest fish: silver on their flanks, dark blue-green on their backs, about 3 feet long at maturity. But considerable effort has been made to keep them going.

Government hatcheries release millions of fall-run Chinook each year into the Sacramento Valley's rivers and streams, launching their annual pilgrimage to the Pacific.

The drought turned their world upside down. Fearing the babies would not survive the unusually warm and shallow waters of the Sacramento River, the Coleman National Fish Hatchery in Anderson last year trucked millions of juvenile salmon to the Delta, the point at which they completed their journey to the ocean. The process was repeated last month.

"It's to keep the fish alive," said Brett Galyean, acting project manager at Coleman.

Despite those efforts, one of the four seasonal runs of Chinook salmon remains in considerable jeopardy.

The winter-run salmon, unlike the fall-run variety, mostly spawn in the wild, laying their eggs in shallow underwater gravel beds. Listed as endangered by the federal government since 1989, the breed suffered devastating losses last year. About 95 percent of the juveniles died off because the water pouring out of Lake Shasta, which feeds the watersheds of the Sacramento Valley, was warmer than predicted.

"They're very susceptible to warm water," said Jeffrey Mount, a professor emeritus at UC Davis and senior fellow at the Public Policy Institute of California's Water Policy Center.

The U.S. Bureau of Reclamation, which operates Shasta, thought it had developed a plan for this year's water releases that would keep the reservoir cool. But in the past two weeks it discovered that Shasta, deprived of snowmelt after a historically warm winter, again was running too warm.

Ron Milligan, the bureau's operations manager for the Central Valley Project, said the solution is to revamp the water-release plan, even if that creates "a lot of anxiety" among farmers and others about supply. A new plan is expected within days. The government, he said, cannot take the chance of a second year of massive die-offs; winter-run Chinook generally live only three years.

With so much water already released from Shasta this spring, Mount and Rosenfield question whether this year's crop of juveniles can be saved.

"Last year's wild class is pretty much lost," Rosenfield said. "The year before that, it wasn't that great of a year. If you lose this year's spawning class, (it's) two-and-a-half strikes. Three strikes and you are out. We are coming up close to extinction on a fish that doesn't live anywhere else."

In California's complicated ecosystem -- much of it engineered by humans -- trying to fix one problem often leads to other consequences. Restricting releases from Shasta means there might not be enough water flowing through the system to prevent ocean salt water from encroaching on the Delta.

To fix that, the Bureau of Reclamation may release additional water out of Folsom Lake. That's triggering alarms from the cities of Roseville, Folsom and other Sacramento suburbs that rely on the lake.

In addition, drawing down Folsom Lake eventually would lead to warmer water in the American River. That could make life difficult for steelhead trout, which are listed as threatened. Just like the winter-run salmon, steelhead suffer when the water heats up.

"When the temperature gets warm, they become more susceptible to disease," said Tom Gohring of the Sacramento Water Forum, an alliance dedicated to preserving the region's water. "A lot of them are just sort of going to go quietly in the night.

"Most ecologists believe the species is not going to blink out because of the drought of 2015," he added. "But it moves us closer to that possibility."

(c)2015 The Sacramento Bee