EUREKA, Calif. - A federal court has ruled that National Marine Fisheries Service failed to protect thousands of whales, dolphins, porpoises, seals, and sea lions from U.S. Navy warfare training exercises along the coasts of California, Oregon and Washington.

In an opinion released late Wednesday, Magistrate Judge Nandor Vadas, U.S. District Court for the District of Northern California, found that NMFS’s approval of the Navy’s training activities in its Northwest Training Range Complex failed to use the best available science to assess the extent and duration of impacts to whales and other marine mammals. The decision requires the federal agency to reassess its permits to ensure that the Navy’s training activities comply with protective measures in the Endangered Species Act.

“This is a victory for dozens of protected species of marine mammals, including critically endangered Southern Resident orcas, blue whales, humpback whales, dolphins and porpoises,” said Steve Mashuda, an Earthjustice attorney representing a coalition of conservation and Northern California Indian Tribes. “NMFS must now employ the best science and require the Navy to take reasonable and effective actions to avoid and minimize harm from its training activities.”

The Navy uses a vast area of the West Coast, stretching from Northern California to the Canadian border, for training. Activities include anti-submarine warfare exercises involving tracking aircraft and sonar; surface-to-air gunnery and missile exercises; air-to-surface bombing exercises; and extensive testing for several new weapons systems.

In 2010 and 2012, NMFS authorized the Navy to harm or “take” marine mammals and other sea life through 2015. The permits allow the Navy to conduct increased training exercises that can harm marine mammals and disrupt their migration, nursing, breeding, or feeding, primarily as a result of harassment through exposure to the use of sonar.

New science from 2010 and 2011 shows that whales and other marine mammals are far more sensitive to sonar and other noise than previously thought. In permitting the Navy’s activities, NMFS ignored this new information. The court found that the agency violated its legal duty to use this “best available data” when evaluating impacts to endangered whales and other marine life.

The Court also rejected the agency’s decision to limit its review to only a five-year period when the Navy has been clear that its training activities will continue indefinitely. The Court held that NMFS’s limited review “ignores the realities of the Navy’s acknowledged long-term, ongoing activities in the [Northwest Training Range],” because “a series of short-term analyses can mask the long-term impact of an agency action. … [T]he segmented analysis is inadequate to address long-term effects of the Navy’s acknowledged continuing activities in the area.”

“This is an important win for the environment and for the tribes’ traditional, cultural and subsistence ways in their ancestral coastal territories,” said Hawk Rosales, executive director of the InterTribal Sinkyone Wilderness Council. “Marine mammals now stand a better chance of being protected from the Navy’s war testing and training off our coastline.”

According to the ruling, NMFS must now reassess the permits using the latest science, which could trigger a requirement that the Navy do more to protect whales and dolphins in its ongoing training exercises.

“The Navy’s Northwest Training Range is the size of the state of California, yet not one square inch was off-limits to the most harmful aspects of naval testing and training activities,” said Zak Smith, staff attorney for NRDC. “NMFS relied on faulty science when approving the Navy’s permits and thousands of marine mammals suffered the consequences.”

“Today’s ruling gives whales and other marine mammals a fighting chance against the Navy,” said Miyoko Sakashita, oceans director at the Center for Biological Diversity. “This ruling means that the Navy must take greater precautions to protect marine life.”

The Navy’s mid-frequency sonar has been implicated in mass strandings of marine mammals in, among other places, the Bahamas, Greece, the Canary Islands, and Spain. In 2004, during war games near Hawai’i, the Navy’s sonar was implicated in a mass stranding of up to 200 melon-headed whales in Hanalei Bay. In 2003, the USS Shoup, operating in Washington’s Haro Strait, exposed a group of endangered Southern Resident killer whales to mid-frequency sonar, causing the animals to stop feeding and attempt to flee the sound. Even when sonar use does not result in these or other kinds of physical injury, it can disrupt feeding, migration and breeding or drive whales from areas vital to their survival.

“In 2003, NMFS learned firsthand the harmful impacts of Navy sonar in Washington waters when active sonar blasts distressed members of J pod, one of our resident pods of endangered orcas,” said Kyle Loring, Staff Attorney for Friends of the San Juans. “The use of deafening noises just does not belong in sensitive areas or marine sanctuaries where whales and dolphins use their acute hearing to feed, navigate, and raise their young.”

Marcie Keever, Oceans & Vessels program director at Friends of the Earth, added, “Recent research confirms that the 82 remaining endangered Southern Resident orcas use coastal waters within the Navy’s training range to find salmon during the critical fall and winter months. NMFS must do more to assure that the Navy is not pushing these critically endangered orcas and other endangered marine mammals even closer to extinction.”

Earthjustice represents the InterTribal Sinkyone Wilderness Council, Center for Biological Diversity, Friends of the Earth and Friends of the San Juans and has partnered with the Natural Resources Defense Council in the lawsuit.