On Feb. 12, 1841, a pod of melon-headed whales swam into the shallow blue waters of Hilo Bay off the rock-ribbed shore of Hawaii’s Big Island. Native Hawaiian fishermen paddled seaward toward the tightly packed pod, trapping dozens of animals between the lava rock and their wooden canoes. Then, banging against the hulls, the Hawaiians began to make a great noise.

“The fish seemed completely bewildered and exhausted from fright,” wrote Charles Wilkes, a U.S. naval officer and explorer who witnessed the hunting ritual and recorded it in his journal.

About 20 melon-headed whales, an inky black species of dolphin rarely seen by humans because of its preference for deep waters, were beached that afternoon. Before the Hawaiians rendered the oil from the blubber and prepared the animals for a feast, Wilkes measured the length of one of the torpedo-shaped carcasses at over 8 feet.

More than a century and a half later, noise pollution of a different origin is thought to have driven almost 200 melon-headed whales dangerously close to another Hawaiian shore. On the Fourth of July weekend in 2004, a large dolphin pod appeared in Hanalei Bay, slapping their tails and swimming in circles off the island of Kauai’s North Shore. Marine scientists mobilized a flotilla of kayaks and outrigger canoes to gently shepherd the distressed animals back out to sea. One young dolphin died.

At the time, the U.S. Navy was in the area using active sonar as part of the world’s largest maritime warfare training event. The sound waves from sonar, used to track enemy submarines, have the potential to harm or kill marine mammals that rely on sound to communicate, navigate and otherwise survive. Animals exposed to sonar have been known to react by swimming for hundreds of miles or rapidly changing their depth, which can cause their eyes and ears to bleed. Whales and dolphins sometimes beach themselves in an attempt to get away from the noise. The psychological effects are mostly unknown.

After extensive study, federal marine scientists concluded in a 2006 report for the National Oceanic and Atmospheric Administration that military sonar was “a plausible, if not likely, contributing factor” to the unusual near stranding in Hanalei Bay. There was no other likely cause.

Hawaii is the most isolated population center on earth. The world’s widest expanse of uninterrupted ocean surrounds the island chain, which is home to several endangered marine mammals and exotic species of fish found nowhere else. It’s there that the U.S. military brings together 47 warships, six submarines, 200 aircraft and 25,000 sailors from 22 nations every two years for a monthlong ocean security training event called Rim of the Pacific Exercise, or RimPac. Activities include dropping underwater explosives and blasting high-frequency sonar.

Smaller-scale Navy training exercises are conducted in Hawaiian waters year round. For these activities, the Navy is not required to announce when or where it uses sonar.

In September the Navy agreed to limit and in some places ban its use of sonar and explosives off Hawaii and Southern California after U.S. District Court Judge Susan Oki Mollway ruled in favor of environmentalists who filed lawsuits claiming the Navy gravely discounted the danger its training events pose to cetaceans. She wrote in her ruling that the National Marine Fisheries Service permitted the Navy to kill certain whale and dolphin populations at rates that could jeopardize their ability to survive.

For environmentalists, that settlement was a small but significant win. The Navy will still blast sonar in the Pacific, but some sensitive whale habitats will be blasted less frequently or not at all.

“We can protect our fleet and safeguard our whales,” said Rhea Suh, the president of the Natural Resources Defense Council, whose lawyers challenged the Navy’s activities in the Pacific on behalf of numerous environmental groups. “This settlement shows the way to do both, ensuring the security of U.S. Navy operations while reducing the mortal hazard to some of the most majestic creatures on earth. Our Navy will be the better for this, and so will the oceans our sailors defend.”

Lt. Cmdr. Matt Knight, a U.S. Pacific Fleet spokesman, said the limitations preserve training and testing activities that he says are critical to national security. More than 40 nations have the kind of modern, extremely quiet submarines that require active sonar as the most effective means to track them, he said. Failure to do so can cost lives. This was most recently demonstrated in March 2010, when the South Korean warship Cheonan was torpedoed by a North Korean submarine, killing 46 sailors.

“The Navy cares about marine mammals. We share the seas with them 24 hours per day, seven days a week,” he said. “No ship commander wants to injure a marine mammal.”

What remains unseen is whether or to what degree the new limitations on underwater explosives and sonar blasting will improve conditions in Hawaii for dolphins and whales.

In the last 15 years, there have been 187 recorded cetacean strandings around the main Hawaiian islands. None of those animals survived. Determining the cause of a stranding is difficult. Beached carcasses quickly decay, which often interferes with scientists’ ability to determine a cause of death. Globally, there have only been a handful of strandings that are attributed to active sonar use, and most have been mass events associated with naval training. In Hawaii the closest link between sonar and marine mammal distress is the near stranding of the 200 melon-headed whales in Hanalei Bay.

Over the last five years, the Navy has committed about $160 million to help scientists — and the military — better understand which cetacean species react to Navy sonar exercises, what types of reactions occur and the duration and magnitude of these responses. More than $2.5 million in Navy-funded marine mammal monitoring research has been conducted off Hawaii and Southern California so far this year.

Still, not much is known about how different species react to one-time sonar exposure versus repeated exposure. As the Navy adjusts where and how often it blasts sonar in the Pacific, this area of study is becoming increasingly critical.

Robin Baird, a marine biologist who leads Navy-funded studies on the interplay between marine mammals and underwater noise for the Cascadia Research Collective in Olympia, Washington, said last month’s settlement may have unintended consequences. It’s feasible, he said, that by agreeing to reduce the frequency of sonar events in some Hawaiian waters, the Navy could cause local dolphins and whales more harm than good.

He speculated that stationary whale and dolphin populations in Hawaii that are repeatedly exposed to sonar throughout their lifetime gradually become less startled by sonar the more they hear it. The corollary to this theory is that marine mammals that pass through areas where sonar is being blasted might be more likely to startle in reaction to the foreign noise. If the frequency of sonar events in certain Hawaiian waters is significantly reduced, he reasoned that resident animal populations that appear to have grown accustomed to the noise might begin to act out.

“If you reduce the use of sonar, you’re going to have more calves who have never heard sonar who are effectively going to have greater risk than if they were exposed [more frequently] and had developed some understanding of it,” Baird said.

It’s a complicated situation. Until more is known about the relationship between marine mammals and noise pollution, he said, it’s feasible that numerous small resident whale and dolphin populations off Hawaii might suffer under the new sonar limitations that seek to protect the animals.

“The only way you’re going to protect those populations, in my opinion, is if you completely exclude sonar from the range of those populations,” Baird said. “I’m not convinced that limiting it is going to provide any meaningful protection.”