The 9th U.S. Circuit Court of Appeals on Friday night rejected the Navy's appeal of restrictions that banned high-powered sonar within 12 nautical miles of the coast and set other limits that could affect Navy training exercises to begin this month.
Also on Friday, a federal judge in Hawaii issued a similar ban for that state's coastline.
In the California case, the appellate judges let stand most of a lower court injunction that set the limits, but altered two restrictions that the Navy argued could harm the readiness of its ships for combat.
Conservation groups that had sued to block the Navy's use of high-powered sonar said the decision was a victory for their side.
"The court is saying that neither the president nor the U.S. Navy is above the law," Joel Reynolds, director of the Marine Mammal Protection Project at the Natural Resources Defense Council, said in a statement Saturday.
"The court found that the Navy must be environmentally responsible when training with high intensity sonar, and that doing so won't interfere with military readiness," he said.
The Navy has argued that additional restrictions would hamper its ability to train effectively.
"In ordering additional mitigation to reduce the risk to marine mammals, the order shifts the risk to sailors and Marines," Capt. Scott Gureck, a Navy spokesman, said in a statement responding to the Hawaii ruling.
Southern California's coastal waters are home to dozens of species of whales and dolphins, seals, and sea lions. Nine species are federally listed as endangered or threatened.
The appellate court said the Navy has acknowledged that high-powered sonar may cause hearing loss and other injuries to marine mammals. The court said the Navy has estimated that its Southern California exercises would expose more than 500 beaked whales to harassment and would result in temporary hearing loss to thousands of marine mammals.
The ban requires the Navy to limit the decibel levels of its sonar under certain ocean conditions and to stop using it altogether when a marine mammals is detected within 2,200 yards of a sonar source.
The Navy said those restrictions would limit its ability to conduct anti-submarine warfare training and possibly prevent certification of some naval strike groups preparing to deploy to the Persian Gulf.
The appellate court staggered the sound-level reductions during certain ocean conditions and tied them to the proximity of a marine mammal. The court also said the Navy can continue to use sonar - although at a lower sound level - when a marine mammal is within 2,200 yards if the sonar is being used "at a critical point in the exercise."
In the Hawaii decision, U.S. District Judge David Ezra ordered the Navy to look for marine mammals for one hour each day before using sonar, employ three lookouts exclusively to spot the animals during sonar use and stop sonar transmission altogether when one of the mammals is within 500 meters, which is nearly 547 yards.
The Navy plans to conduct as many as 12 exercises off Hawaii over the next couple of years. Navy officials say Hawaii waters provide a unique environment that includes both deep and shallow water for training.
The Navy undertakes "extensive measures" to protect marine mammals during training and is considering asking for more review, possibly by the U.S. Supreme Court, said spokeswoman Lt. Cmdr. Cindy Moore.
"We're a country engaged in two wars. When we send America's sons and daughters into harm's way, we must ensure they have the best possible training," she said.