Wanger's ruling also said the U.S. Fish and Wildlife Service didn't follow its own regulations, which require the agency to study whether the pumping reductions are economically and technologically feasible.
The judge has been harshly criticized by water users for some preliminary rulings that favored the environmental protections. On Tuesday, plaintiffs who had sued to overturn the plan applauded his latest decision although it doesn't necessarily mean they will get more water.
The ruling is a "step closer to accomplishing California's coequal goals of restoring the Delta environment and ensuring that the public will have an adequate and reliable water supply," said Tom Birmingham, general manager of the Westlands Water District.
The politically conservative Pacific Legal Foundation which joined the smelt battle when it filed a separate lawsuit on behalf of three San Joaquin Valley farming operations issued a statement from attorney Damien Schiff that said Wanger was "correct to recognize" that the smelt plan "involved a lot of junk science."
"The feds claimed that the pumps harm the smelt population, but they didn't provide any meaningful measurement to back up that assertion," Schiff said.
While the ruling looks to be a victory for agricultural water users and their urban water-district allies, the ruling also turned back a number of their legal challenges.
And even though significant portions of the smelt plan will likely have to be rewritten, it doesn't necessarily mean more water for Los Angeles and Bay Area water agencies and agricultural users on the San Joaquin Valley's west side.
These water users have battled environmental groups who sought to keep the smelt plan in place, saying it was vital to protect the tiny fish.
"We're disappointed that the judge found the number of flaws that he did with the [smelt plan]," said George Torgun, an attorney with Earthjustice, which is one of the groups fighting to keep smelt protections in place. "We think it was based on sound science."
Still, Torgun said he was pleased that Wanger continued to agree with the contention of environmentalists and the federal government that delta pumping operations do hurt the tiny fish.
Wanger has issued several preliminary rulings in the case, but this was the big decision that both sides had awaited. It came more than four months after the oral arguments in the case.
But this is unlikely the final word in the long-running battle which Wanger's ruling called a "continuing war over protection of the delta smelt" that has pitted environmentalists against the urban and agricultural users that depend on the delta for their water supply.
For starters, Wanger has ordered both sides to convene Jan. 4 to see what, if anything, needs to be done while the U.S. Fish and Wildlife Service rewrites the smelt plan.
This will likely lead to more arguments between the two sides, and possible orders from Wanger affecting smelt-related pumping restrictions that could kick in as early as this month.
In addition, any new smelt plan could face additional court challenges from either environmentalists or water users.
And there also is the parallel issue of endangered salmon, which also have a protection plan that is being challenged by water users. Arguments in that case are scheduled Thursday and Friday before Wanger.
The battle over the smelt plan known as a "biological opinion" dates to earlier this decade, when an earlier version was drawn up by the U.S. Fish and Wildlife Service in response to a U.S. Bureau of Reclamation water management plan for the delta. That initial biological opinion found that both the Central Valley Project and the State Water Project would not hurt the delta smelt or its habitat.
In February 2005, the Natural Resources Defense Council and five other environmental groups sued the Fish and Wildlife Service in response to that initial opinion. Wanger in May 2007 agreed with the environmentalists, finding the plan was legally flawed.
The ruling sent the U.S. Fish and Wildlife Service back to the drawing board, and in late 2008 it issued a revamped biological opinion. The new plan was a complete turnaround from the one in 2005. It found the water projects were "likely to jeopardize the continued existence" of the delta smelt, as well as "adversely modify" its critical habitat.
Water users, including Westlands, in turn sued after the new biological opinion resulted in severe pumping cutbacks. That eventually led to Tuesday's ruling. But Torgun, the Earthjustice attorney, said this Wanger ruling "doesn't feel like 2007."
Though Wanger's ruling will lead to a reworking of the smelt plan, he said, it will not be a radical rewrite and will still contain the core finding of the last one that the delta pumps are a danger to the smelt.
"I don't see that big of a change this time around," he said. "But it's a bit disappointing that it has to be redone."
In a sharply worded, 255-page decision, U.S. District Judge Oliver Wanger, of Fresno, concluded: "The public cannot afford sloppy science and uni-directional prescriptions that ignore California's water needs."
He ordered regulators to rewrite significant portions of a permit for massive Delta pumps that deliver water to the Bay Area, San Joaquin Valley and Southern California. The permit sets out a host of rules that are meant to prevent Delta smelt from going extinct.
"We are thrilled with the court's decision," said Thomas Birmingham, general manager of the Westlands Water District, the country's largest irrigation district and the region hardest hit by recent drought.
The ruling, Birmingham said, would send the permit back to regulators for "a thorough overhaul."
Wanger characterized the situation as "the continuing war over protection of Delta smelt ... and associated impacts to the water supply for more than half of the state of California."
Despite the blistering language Wanger used at times, it was unclear how much relief water agencies most affected by the regulations would see. He ordered no immediate changes to the pumping regulations.
His ruling appeared to echo a critique in March by a panel convened by the National Academy of Sciences that found the new Delta smelt permit along with a related permit to protect salmon, steelhead and green sturgeon was conceptually justified but inadequate in its specifics.
Although he was more critical, Wanger, like the panel of scientists, determined regulators were correct to put limits on how hard the pumps could drive two Delta rivers to run in reverse. But both were critical of how government biologists justified the specific limits they laid out. Wanger ordered the U.S. Fish and Wildlife Service to adjust and better justify those limits.
Similarly, a new restriction that requires more water to flow through the Delta in the fall to reduce salinity was justified but no scientific rationale was given for the specific salinity limits that were set.
"It's disappointing and frustrating a lot of sound and fury but it might not be as bad as I thought and it might not be as good for the contractors as they think it is," said Doug Obegi, a staff attorney for the Natural Resources Defense Council who worked on the case.
Obegi predicted changes ordered by Wanger would not allow state and federal water projects to return to the record-breaking pumping levels they reached from 2000 to 2007. It is possible, Obegi said, that the rewrite might even result in tighter restrictions.
Wanger also was sharply critical of the permit's assertion that pumping exacerbates other problems in the Delta by altering flow patterns and habitat. Biologists contend the pumps change the Delta's hydrodynamics in ways that foster undesirable weeds, fish, algae and clams and increase the exposure of fish to pollution.
Wanger called those connections "unsupported."
A hearing is scheduled in early January to determine the next steps. After Wanger invalidated the previous permit in 2007, he held a series of technical hearings to set interim pumping limits until a new permit was written in late 2008.
It is unknown whether he will follow the same pattern this time.
Mike Taugher covers the environment. Contact him at 925-943-8257.