More than 60 disoriented dolphins swam into ankle-deep waters off the Florida Keys near the town of Marathon on 2 March, prompting a massive rescue operation involving wildlife officials and dozens of volunteers.
Some of the mammals have been led back to deep water. But about two dozen others have died or have been euthanized to stop their suffering.
More dolphins are being taken care of by biologists and park rangers.
Nobody knows what caused the dolphins to beach.
But US navy and environmental officials said they were looking into the possibility that top-secret exercises involving the USS Philadelphia, a Los-Angeles-class attack submarine, had something to do with the beachings.
"The navy takes this very seriously and is, of course, interested in the outcome" of the investigation, Senior Chief Gregg Snaza, a spokesman for the US Fleet Force Command, said in a telephone interview from Norfolk, Virginia.
Snaza said the National Oceanic and Atmospheric Administration was leading the inquiry, but the military was concerned about the incident and was providing full cooperation as it waits for the results of necropsies.
The Philadelphia, which is reported to have been about 65km off the Florida Keys on Wednesday, had on board a group of SEAL commandos, one of the elite US special operations teams trained to stealthily penetrate enemy territory, often from submerged vessels.
"They were working with the SEALs in support of special ops forces. That is one of the many missions our attack submarines are capable of doing"
Senior Chief Gregg Snaza,
spokesman for the US Fleet Force Command
Snaza declined to describe the nature of the mission but said it was "an interoperability exercise" designed to fine-tune cooperation between components of the navy.
"They were working with the SEALs in support of special ops forces," he said of the Groton, Connecticut-based submarine crew. "That is one of the many missions our attack submarines are capable of doing."
The spokesman could not confirm or deny whether sonar was used by the Philadelphia, saying: "The navy is researching that."
Navy causing distress
Scientists and environmental activists repeatedly have said that powerful high-pitched sonars used by navy surface ships and submarines for navigation and targeting purposes is causing distress among marine mammals such as whales and dolphins, deafening and disorienting them and, eventually, prompting their mass stranding.
The navy's experiments with powerful sonars became front-page news in March 2000, when members of four species of whales stranded themselves on beaches in the Bahamas after a US naval battle group used active sonar in the area.
Investigators later found that the whales were bleeding internally around their brains and ears, according to environmental activists.
Last year, the European Parliament called on the EU's 25 member states to stop deploying high-intensity active sonar until more is known about its environmental impact.
But the US navy insists high-intensity sonar is important for the success of its missions.