Senior water rights for the South San Joaquin Irrigation District were protected once again in a federal court decision.

While the 9th Circuit Court of Appeals on Monday upheld a 2009 federal decision that called for reducing the amount of water pumped from the Delta in order to protect salmon and other species, it left intact a lower court ruling that said the federal government couldn’t use SSJID or Oakdale Irrigation District water to pump up flows for fish.

The ruling opens the door for water beyond the 600,000 acre feet the two districts share from New Melones Reservoir to be used to maintain fish flows. That means water districts such as Stockton East and Stockton Central may go without water in years when runoff is light and more water for fish is required.

The 2009 environmental review by the National Marine Fisheries Service found that continuing to pump water from the Delta at such a high rate would threaten several endangered salmon species and killer whales.

Some of the state’s biggest water agencies, including Southern California’s Metropolitan Water District, had challenged the 2009 federal decision. A lower court had invalidated part of the National Marine Fisheries Service’s review but allowed the reduced pumping to remain in effect.

The court decision affirmed the original 2009 federal decision reducing the pumping.

Federal fisheries officials, representatives of the state fishing industry and environmental groups welcomed the news.

“Today’s federal court of appeals ruling upholds protections for salmon, steelhead trout, killer whales and other wildlife that rely on natural river flows in California’s Central Valley and a functioning delta to survive,” said John McManus, executive director for the fishing industry’s Golden Gate Salmon Association.

Federal biologists in 2009 said water withdrawals from the delta were driving endangered killer whales off California closer to extinction by reducing salmon and other fish the killer whales depend on for food.

Daniel O’Hanlon, a lawyer for the water districts, did not immediately return a request for comment.

The court decision counters scientific evidence that research firms such as Fishbio have gathered monitoring Chinook salmon.

While the ruling centers on exporting water out of the Delta to the Southland, the federal government’s rationale also calls for more water to be released from river storage feeding into the Delta for fish migration.

The federal government — in a move questioned by some biologists as to its effectiveness — released 25,000 acre feet of water in October from New Melones during the fall run of Chinook salmon in the Stanislaus River.

That’s enough water to supply the domestic needs of the cities of Manteca, Ripon, and Escalon for more than three years or 331,000 Californians for a year,

And while it is being done in the name of helping the fish, biologist Andrea Fuller with Fishbio notes more than 10 years of intense studies show it will have a negligible impact if even that. And ultimately it could hurt fish.

Once the water flows out of the Stanislaus and into the San Joaquin River south of Manteca the state considers it abandoned and up for grabs.

“The planned higher flow only happens one percent of the time (naturally),” Fuller noted in September. “They (the federal government) are making a release equivalent to the wettest year possible in a year of severe drought.”

That is on top of the regular 200 cubic feet per second that flows down the Stanislaus in October.

The flow requirement stems from federal edicts aimed at protecting the Chinook salmon.

Fuller, who has spent 20 years studying the Stanislaus River, noted the federal government hasn’t provided any scientific data to back up their edict despite numerous requests to do so.

SSJID in partnership with Oakdale Irrigation District has spent more than $1 million over the past several years studying fish on the Stanislaus River. SSJID General Manager Jeff Shields has said he’s confident that the Stanislaus River “is the most studied river” in the state when it comes to fish.

Fuller said there is a concern that the federal strategy will be counterproductive. If higher flows entice more fish than the Stanislaus ecological system can handle, it will lead to fish die off. She noted the habitats on the Merced and Tuolumne rivers are better suited for larger fish numbers.

Fuller’s observations are based on hard data collected from along the Stanislaus. Included is a weir the two districts paid to have installed across the Stanislaus at Riverbank that uses infrared technology to count fish and note what time they pass through and how it relates to water flow and temperatures.

The SSJID draws water from New Melones Reservoir to supply the cities of Manteca, Tracy, and Lathrop as well as to provide irrigation water to 72,000 acres in the South County.

Editor’s note: Associated Press contributed to this report.