Deadline is set on delta water

A Superior Court judge has given the state two months to get environmental permits in the Sacramento-San Joaquin Delta or he will shut down the massive Northern California pumps that kill endangered fish in the process of supplying the Southland with much of its water.

State officials vowed to fight the ruling, predicting dire consequences for the California economy if the pumping stopped.

“It would be unacceptable to curtail all deliveries to the State Water Project,” said Department of Water Resources Director Lester Snow, adding that the project supports a $300-billion share of the state’s economy.

“That’s a lot of farm jobs, industrial jobs and homes.”

The delta supplies 60% of the water distributed by the Metropolitan Water District of Southern California, the region’s major water wholesaler.

Although the state will almost certainly find a way to keep the pumps operating at some level, Thursday’s ruling by Alameda County Superior Court Judge Frank Roesch could force reductions in the flow of water to the south.

It is also likely to move the state another step closer to dramatically overhauling the way it manages water shipments between Northern and Southern California.

“There are obviously things that are going to have to be done,” said Bill Jennings, executive director of the California Sportfishing Protection Alliance, which filed the environmental lawsuit in which the judge ruled. “It’s no longer business as usual.”

The judge agreed with the argument by Jennings’ group that the Department of Water Resources has never gotten the necessary authorization from the California Department of Fish and Game to kill threatened and endangered fish at the delta’s Harvey O. Banks pumping operation. The operation forms the heart of the State Water Project that supplies urban Southern California.

The decision comes at a time of escalating concern over the fate of the delta east of San Francisco and its rapidly declining fish populations.

The tiny, native delta smelt has sunk to record lows during the last three years, and introduced species and native salmon are also struggling.

Research suggests that the pumping operation is a leading cause of the decline in fish, if by no means the only cause.

Despite an elaborate, expensive screening process, fish die at the pumps. To keep salty San Francisco Bay water away from the pumps, the project has altered the delta’s natural salinity levels. The pumps are so powerful that they can reverse the flow of water in the channels that crisscross the delta.

Changes in the pumping regimen intended to protect spawning fish appear simply to have shifted mortality -- killing smelt before they can spawn, or killing the young.

Though the judge’s warning does not signal an immediate crisis for water managers, they are taking it seriously.

“We see this as a strong signal by the judge,” said Jeffrey Kightlinger, the water district’s general manager.

The court order, he said, is another sign that “transporting water through the delta is simply not sustainable in the long run.”

Kightlinger said the water district could tap a large reserve if the pumping is stopped and would not have to resort to immediate rationing.

But, he said, “We’d hate to use that up.”

Kightlinger added, “We will be working with the state very hard to try and make sure they do not shut the pumps.”

The judge’s ruling is the latest development in more than a decade of environmental fights and government programs to fix the troubled delta, a sprawling area that is California’s water crossroads.

“This is a very important event. It really is,” Barry Nelson of the Natural Resources Defense Council said, calling the opinion a landmark.

State officials learned of the decision Friday and in a hastily called news conference said they would ask the judge to give them more time to meet his demands.

They also disputed the judge’s finding that they had never obtained the proper authorizations to kill fish under the state Endangered Species Act.

bettina.boxall@latimes.com