Earthjustice, representing several groups, filed the lawsuit in federal court in Honolulu, only hours after the federal agency announced it had decided to grant the Navy permits to move ahead with its plans for training and testing in the Pacific.
Navy officials estimate its activities would have a negligible impact on marine mammal populations.
Environmentalists dispute that and favor creating zones that would be off-limits to biologically sensitive areas. They also want the Navy to avoid training in certain spots seasonally when they are rich in marine life.
"The science is clear: sonar and live-fire training in the ocean harms marine mammals," said Marsha Green of Ocean Mammal Institute, which is among the groups suing. "There are safer ways to conduct Navy exercises that include time and place restrictions to avoid areas known to be vital for marine mammals' feeding, breeding and resting."
The Navy estimates that its activities could inadvertently kill 186 whales and dolphins off the East Coast and 155 off Hawaii and Southern California, mostly from explosives.
It calculates more than 11,000 serious injuries off the East Coast and 2,000 off Hawaii and Southern California, along with nearly 2 million minor injuries, such as temporary hearing loss, off each coast.
NMFS granted the permits for the Atlantic and Gulf of Mexico last month. The Pacific permit was the final one.
Environmentalists won a small victory in September when a federal judge ruled the marine fisheries agency did not consider the latest science when it granted permits last year.
In Monday's ruling, the agency said it will review the latest scientific data yearly with the Navy to determine if enough is being done to mitigate the risks.
"The Navy is committed to complying with environmental laws and protecting the environment," Navy spokesman Kenneth Hess said when asked about the lawsuit.
Reported mass strandings of beaked whales have increased around the world since the military started using sonar more than half a century ago. The sounds can scare animals into shallow waters where they can become disoriented and wash ashore.
Aside from beachings, biologists are concerned about prolonged stress from changes in diving, feeding and communication habits. Only in the past decade have scientists had the technology to closely monitor the behavior of whales and dolphins.
Two recent studies off the Southern California coast found certain endangered blue whales and beaked whales stopped feeding and fled from recordings of noise similar to military sonar.
Beaked whales are highly sensitive to sound and account for the majority of strandings near military exercises.
Navy officials say it's vital to national security that sailors receive realistic sonar training, and use simulators where possible.
Environmentalists want safety zones that would guarantee no high-intensity sonar activity near marine sanctuaries and areas where blue, fin and gray whales gather seasonally.