A massive Navy training and testing ground offshore the Southeast might just have hit a big shoal.

A federal judge in California Thursday ruled that the federal National Marine Fisheries failed to make sure whales, dolphins and other marine mammals were protected from underwater blasts caused by Navy training there. NMFS didn’t use the best available science to assess potential injuries. The judge ordered the agency to re-do the permits.

The ruling sent shock waves through the environmental, regulatory and military communities. Conservationists long have claimed too many concessions are made by federal environmental agencies when permits are issued for military activities, despite accumulated evidence that the blasts injure and kill the animals.

The ruling has obvious implications for the proposed Atlantic Fleet sea and air warfare-training range along 50,000 square miles off the East Coast, said Michael Jasny of the Natural Resources Defense Council. The range is currently in the process of re-permitting activities there for the next five years.

“You wouldn’t build a highway through the habitat of an endangered species and then act like everything will be hunky-dory in five years,” Jasny said.

“The science is clear, and the impacts on marine mammals are devastating and unacceptable,” said Amelia Vorpahl, of Oceana.

NMFS “is reviewing the United States District Court of California’s ruling regarding the Navy’s training activities in the Northwest training range complex,” spokeswoman Connie Barclay said when asked for comment.

The Navy, too, was taking a hard look at the ruling.

“The Navy is aware of the recent District Court ruling with respect to National Marine Fisheries Service authorization of training activities in the Northwest Training Range Complex, but is not a party to the litigation. At this point we are still studying the ruling and cannot provide further comment. The Navy is committed to complying with environmental laws and protecting the environment,” the military service said in an email statement when an Atlantic Fleet Training and Testing spokesman was asked for comment.

Environmental groups say exercises in the range, where the Navy would sometimes use active sonar and explosives, could deafen and/or be lethal to marine mammals such as whales and dolphins that navigate by echolocation, and could harm other species such as sea turtles.

They worry that intensive training activity could spur “population sinks,” areas where animals die or fail to reproduce, and the depleted area then draws in more animals who do the same.

The Navy has maintained it has conducted training offshore for 60 years with little environmental impact, and has changed how the exercises are conducted when problems have emerged.

Any number of marine mammals, including the critically endangered right whales, frequent the waters off South Carolina and the entire coast. Fewer than 500 right whales are known to exist off the East Coast.

The concern for deafening from sonar, explosives and other loud underwater noises has risen in recent years with reports of strandings that were otherwise inexplicable. For instance, Navy sonar might have killed three dozen whales that later turned up on an Outer Banks beach in January 2005, but an ensuing investigation found no solid evidence.

The Navy has made efforts to refine how it trains to reduce the impacts, and is leading sponsor of impact studies.

In fact, the Navy just completed and released the final environmental impact study for the Atlantic range re-permitting so that the range can be operated with minimal impact on marine species.

The final report must be approved by the Navy and federal environmental agencies. Officials had expected it to be signed off by the January 2014 expiration of the current permits for the range.

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