They have tracked whales by helicopter and, more recently, attached electrodes that will give complex information about what the animals are doing - with the ultimate goal of helping scientists understand why.
Still, "it's definitely a new science," said Amy Scholik-Schlomer, a fisheries scientist with the National Oceanic and Atmospheric Administration. "We've learned a lot. We need to learn a lot more."
NOAA is updating its acoustic-guidance document for marine mammals, setting threshold levels and including other information to help scientists and agencies better predict a marine mammal's response to sound that humans generate in the water.
Scholik-Schlomer said officials hoped to have it done by the fall.
The ocean has always been filled with sound, from the rumble of earthquakes to the whoosh of waves, the sizzle of rain, the crack of lightning, and the song of whales.
"Today, in much of the Northern Hemisphere, commercial shipping clouds the marine acoustic environment with fog banks of noise, and the near-continuous pounding of seismic air guns in search of fossil fuels beneath the surface of the seafloor thunders throughout the waters," wrote Brandon Southall and a colleague in a 2012 editorial.
Southall, president of Southall Environmental Associates, based in Santa Cruz, Calif., is one of the nation's foremost researchers on sound and its effects on marine mammals.
As part of the Rutgers study, scientists will use air guns to release compressed bubbles of air that expand rapidly and release a burst of sound.
Hydrophones will record the returning sound waves, and computers will turn the information into 3-D images, revealing the course of ancient rivers, the shift of coastlines, and the buildup of sandbars as sea level rose and fell as long as 50 million years ago.
The scientists say this will help them better predict what will happen with sea level rise today.
The study was to have begun in early June, but New Jersey fought to stop it. The case is focused on procedural issues - whether the state has the right to review a federal activity that could affect its coastal waters - but state officials have said they feared that the loud sounds could harm marine life and disrupt recreational and commercial fishing, harming the state's lucrative tourist industry.
Two judges have denied New Jersey's request to stop the study. Asked whether work had begun, a Rutgers spokesman said he could not discuss the study while it was in litigation.
Scientists now have arrays of underwater listening devices to follow animals fitted with acoustic tags.
They find that some animals experience a temporary "threshold shift" - the same way a human's hearing might be impaired for a short time after a loud rock concert. Otherwise, Southall said, "we're seeing that for at least some species, the ears appear to be pretty tough."
At least some species, including bottlenose dolphins and some seals, "look like they can take quite a loud sound before their hearing starts to change," he said. Harbor porpoises stick out as being more sensitive than researchers thought.
The pitch of the sound matters. Large whales are tuned to hear sounds at the lower end - akin to the keys of a piano left of middle C. Seismic sounds are in this range, Southall said.
Seals hear more in the mid-range; porpoises hear the higher sounds.
Now, researchers are turning their attention to behavior. Maybe the sound won't hurt the animal's ear, but will it interfere with the ability to hear something else that's important?
And most crucially, if an animal's behavior changes due to sound, is that bad? Does it cost the animal energy or send it to a place that's not as safe?
NOAA's guidance document covers only hearing impacts, Scholik-Schlomer said. Officials are "working on trying to develop guidance for behavior," she said, although that's "more challenging."
The National Marine Fisheries Service, a NOAA division, has given the Rutgers project a permit to "harass" nearly three dozen marine-mammal species of dolphins, whales, and seals.
Harassment could mean that the animals stopped feeding or changed course if they were traveling. Officials do not expect any animals to be killed or permanently injured.
The permit includes procedures for monitoring marine mammals in the area and specifies when the air guns must be stopped to avoid harming the animals.
But critics contend that animals will be harmed.
Bob Schoelkopf, director of the Marine Mammal Stranding Center in Brigantine, New Jersey's first responder to animals that become beached, said he didn't see how observers could possibly know every species in the area.
"Our perspective is that after 135 dolphin deaths last summer in 31/2 months" from a virus, "now we're looking at another problem."
He wants NOAA to set up a fund so that if animals start coming ashore, officials can look for seismic-related injuries, such as inner-ear damage.
He also said that if an animal became disoriented, swam away, and died, no one would ever know. "If they lose an animal, it's going to be shark bait."