The area stretches from the inland waters of Puget Sound to the northern coast of California. It is home to endangered whales such as orcas, humpback and blue, as well as seals, sea lions and dolphins.
"The training is necessary so these units are prepared for their various missions," said John Mosher, Northwest environmental manager for the U.S. Pacific Fleet. "They have to train close to home ports where the vessels are located."
He noted that the Navy has been conducting tests and training in the Northwest for decades.
Its current five-year permit expires in 2015, and the Navy has issued a draft environmental impact statement as it looks to continue, as well as expand, exercises for another five years.
The Navy held public meetings last week in Washington. Four more are scheduled in Oregon, California and Alaska.
The Navy ultimately needs authorization from the National Oceanic and Atmospheric Administration under the Marine Mammal Protection Act, since explosive detonations, sonar and vessel strikes have the potential to disturb, injure or kill marine mammals.
"Nobody is trying to deny the Navy the opportunity to prepare themselves appropriately," said Kyle Loring, a staff attorney with Friends of the San Juans based in Friday Harbor, Wash.
But he said there should be limits to where and when the exercises occur. His nonprofit environmental group and others have urged the Navy to limit the areas and times when it trains to protect endangered orcas and other species, saying noise from sonar can harass and kill whales and other marine life.
In its draft report, the Navy says the use of sonar and other active acoustic sources for testing may expose marine mammals to sound levels that could potentially injure them. It would also expose them to many more instances that could disrupt their behaviors.
The Navy's preferred alternative proposes 30 bombing exercises a year, as well as increased air-to-surface missile exercises and anti-submarine tracking activities that use sonar.
"It does sound alarming when we say we're dropping bombs. With that said, there's little bombing activity with live explosives," Mosher said, noting that live bombs haven't been used in the training complex in the last three years but the Navy still has to plan for their use.
"In reality we don't typically do as much as we permit for," he said.
The Navy currently sets up a safety zone around vessels that use sonar, shut down sonar use if marine mammals are seen within designated safety zones and use lookouts to help spot marine mammals.
"We want them to use the best available science as they go forward with this new process," said Kristen Boyles, an attorney with Seattle-based Earthjustice, which sued NOAA's National Marine Fisheries Service in 2012 on behalf of several groups.
The groups asked a federal court to order the fisheries service to study the long-term effects of sonar on marine mammals.
Last fall, a federal judge in San Francisco said the fisheries service failed to consider the best available scientific data when approving permits for the Navy in 2010. He set an August deadline for the agency to reassess how it will protect whales and other marine life.
Last month, attorneys for the federal agency filed a notice of appeal last month.