Record Staff Writer
June 14, 2009 6:00 AM

At mile 59 on the Stanislaus River, the few steelhead struggling upstream to spawn encounter a solid wall: Goodwin Dam.

It is here that two San Joaquin County water districts divert flows in an urgent effort to satisfy a growing population and refill a sagging underground aquifer.

And it is a bit farther upstream, at towering New Melones Dam, where new rules to protect the fish might quash Stockton’s 26-year effort to secure that critically-needed water.

The rules require year-round flows for fish downstream of Goodwin, meaning less water can be stored for San Joaquin County at New Melones Lake. An attorney for Stockton East Water District, which sends water to Stockton, said last week that the district can now expect no water at all for many years.

The rules, announced earlier this month by the National Marine Fisheries Service, stunned water officials.

“They just want the water, and they’re going to take it,” said Stockton East General Manager Kevin Kauffman, who predicted the federal government will get sued by just about “everybody” as a result of their sweeping regulations.

“It’s just the beginning,” Kauffman said.

Even if the rule stands, do not expect the taps to run dry tomorrow. In addition to the Stanislaus, Stockton draws water from the Calaveras River and below ground.

But this region has been searching for a more secure water supply for decades, and millions have been spent pursuing the Stanislaus.

Contracts for the water were signed Dec. 19, 1983. Former Stockton East manager Ed Steffani still remembers the celebration that night.

“It was a sure bet we were always going to get water,” he said.

It took several years to build the $65 million tunnel needed to take the water from one basin to another. Then, just as the spigots were ready to open, new environmental safeguards for fish required more water be sent downstream.

All told, since 1993 Stockton East and its neighbor, the Central San Joaquin Water Conservation District, have received their full allotment of Stanislaus water just once – in 2006. They were shut out completely in 1993, 1994 and 2004, and most years have gotten less than half of the contracted amount.

A $500 million lawsuit was filed against the U.S. Bureau of Reclamation, but the districts lost. An appeal is pending and a ruling could come any day, an attorney said.

The new rules were required after a federal judge threw out old ones, calling them inadequate. The rules include prescriptions for several species of fish throughout Northern California, with the consequence of a 5 percent to 7 percent decline in water exports from the Delta.

But with the Stanislaus it is all about steelhead. And if Stockton has gotten a raw deal, so have the fish.

Before 1850, there were probably 1 million to 2 million steelhead spawning in Central Valley waterways. Most recently, there were 3,628 spawners, according to a 2005 study.

In 2006-07, no more than 12 adult steelhead were seen passing through a weir on the Stanislaus, compared with more than 3,000 fall-run chinook salmon, according to the Fisheries Service analysis. And very few juvenile steelhead make it out of the river alive.

Among the many problems, according to the analysis by the National Marine Fisheries Service:

» Construction of the dams blocked the river from transporting gravel downstream; gravel beds are good spawning habitat.

» Consistent, uniform releases of water from the dam make floods less frequent. Floods help shape the river to create a variety of habitat and make it easier for fish to avoid predators.

» River temperatures are too warm for juvenile steelhead as they float downstream.

Federal biologists’ solutions include greater flows, injection of enough gravel to fill the beds of 50,000 pickups, and a study of whether, someday, steelhead might gain passage above the dams to their historic spawning grounds.

The goal is not to drain New Melones Lake, said Rhonda Reed, a scientist with the Fisheries Service.

“We need to be able to help (the Bureau of Reclamation) do their job in such a way that it doesn’t jeopardize the fish,” she said. “And it’s hard. A dry reservoir is not good for fish, and it’s not good for people.”

The Fisheries Service predicted diversions to San Joaquin County could decrease by 22 percent.

But Stockton East attorney Jeanne Zolezzi argues that models used by the feds are flawed and that for “many years” in the future no water will be delivered to the county. In a wet year, she said, New Melones could be drawn down by more than 600,000 acre-feet to protect fish – that is one-quarter of the reservoir’s capacity and more than half of its average runoff.

No water from the Stanislaus means about half of the surface water coming into Stockton is eliminated.

“We have deep, deep concerns about this,” said Mark Madison, director of the Stockton Municipal Utilities Department. “We need more than what the Calaveras (River) will provide.”

The city wants to suck water directly from the Delta, but that project is still in the planning phase.

Reclamation, which operates the Central Valley Project of which New Melones is a part, acknowledges that it overestimated how much water would be made available by constructing the reservoir and signing contracts with the water districts.

Spokesman Pete Lucero said the bureau still is analyzing the impacts of the 844-page Fisheries Service opinion.

But he said: “It does appear that the impact may be significant.”