PHOTO: WAYNE LEVIN/GETTY IMAGES

It was a haunting sight. On a cold, gray day in January 2005, along a remote stretch of beach on North Carolina's Outer Banks, dozens of pilot whales began to run themselves onto the sand. Eventually 34 of the jet-black, two-ton animals lay dead. The following day, three more whales—a newborn Minke whale and two dwarf sperm whales—washed up nearby.

Although whales can strand for various reasons, including sickness and disorientation, public speculation over the North Carolina stranding quickly zeroed in on a single culprit: military sonar. The U.S. Navy had been conducting a training exercise in the area around the time of the event, and an initial report by the National Marine Fisheries Service, which investigates strandings, listed sonar as a possible cause for the incident (the final report on the stranding was due out as this issue went to press). The Navy stated that the exercise took place about 100 kilometers from where the whales beached, too far to have had any effect. More than a year after the stranding, though, doubts still linger.

Not too long ago, the very idea that intense sound could do bodily harm to ocean creatures would have seemed bizarre, even to those who study marine mammals for a living. "If you had asked anyone 15 years ago, even 10 years, everybody would have said, 'That's a crazy idea,' " says Robert Gisiner, program manager for marine mammal science and technology at the Office of Naval Research (ONR), in Arlington, Va. Now Gisiner and other whale experts say they have no doubt there's a link, at least between certain types of sonar systems and certain types of whales. In the last couple of years, the International Whaling Commission (IWC) and the Pentagon's JASON scientific advisory panel—groups not necessarily known for their nature-friendly stances—have also noted with concern sonar's harmful effects on cetaceans. "It's been a journey of surprises," Gisiner says.

Among the "surprises": in 1996, 12 Cuvier's beaked whales washed up along a 40-kilometer stretch of beach in western Greece, following a NATO training exercise in the Mediterranean Sea. Four years later, on the heels of a Navy exercise, four different species of whales stranded in the Bahamas. And in 2002, after a number of beaked whales stranded during a multinational naval exercise in the Canary Islands, necropsies found hemorrhaging around the animals' ears and lungs and unusual gas bubbles in the blood and internal organs. Also anomalous about all three strandings was that they occurred over large areas and involved species that rarely strand in groups. By some counts, dozens of other whale strandings and an unknown number of whale deaths have been linked to military sonar [see photo, "Dead Calm"].

What's less surprising, perhaps, is that the whales-versus-sonar controversy has spun into a public relations nightmare for the Navy. Environmental groups, most notably the Natural Resources Defense Council, in New York City, have taken the Navy to court, and letter and e-mail campaigns—not to mention the occasional stranding—ensure the issue is never out of the news for long.

The Navy, for its part, contends that it needs so-called active sonar to detect the latest generation of "quiet" submarines—diesel-powered machines that, when running on batteries, generate virtually no noise. Active sonar systems emit intense waves of acoustic energy into the water and then listen for the returning signals, and they are "the only way to detect diesel subs in certain situations," says Capt. William Toti, the officer in charge of the Fleet Anti-Submarine Warfare Command, based in Norfolk, Va. Forty countries now have such subs, although the United States is more concerned about those that might acquire the vessels in the future, Toti says.

The sonar controversy has also focused attention on a broader issue: oceans everywhere are getting noisier because of commercial shipping, underwater oil and gas exploration, and other human activity, and scientists have no clear idea what harm these man-made noises pose to whales and other sea creatures. "The strandings are important because they raise the profile of noise," says Sarah Dolman, science officer with the Chippenham, England­based Whale and Dolphin Conservation Society. "But they may be just the tip of the iceberg."