The depth charge was at the bottom of the trawling net, covered with mud and hidden under the blind fish and pale-skinned invertebrates that John Musick had just dredged from the floor of the Atlantic 2 1/2 miles below. After 30 years rusting off the coast of New Jersey, the bomb still was capable of blowing a 300-foot hole in Musick's 150-foot research vessel.

"That was kind of unnerving," said Musick, a senior marine expert at the Virginia Institute of Marine Science. "We got it overboard as fast as we could."

Musick has been hauling the odd works of man and nature from the deepest parts of the Atlantic for 12 years. He is paid to study ocean garbage dumps and the effect they have on the sea life around them.

Last month, Musick and other environmentalists charged that a Navy proposal to sink five decommissioned nuclear submarines in the ocean could endanger not only sea life, but the commercial fishing industry and seafood consumers.

"You are dealing with high-level, not low-level radiation," says Musick, who has studied other Atlantic sites where radioactive material has been dumped, including a spot off the coast of Maryland where Sea Wolf, the world's second atomic-powered submarine, was secretly sunk in 1959. "If there is any radioactive leakage, fish are one possible mode of transportation away from a dump site into shallow water."

Navy officials say the alarms are premature and exaggerated. Before any of the five drydocked submarines are scuttled, their nuclear fuel and reactors would be removed. The stainless steel container plants remaining would emit only low levels of radiation, says the Navy, and would be sunk too deep to present any danger to the ocean's ecosystem.

Whether the submarines would emit high- or low-level radiation has not been publicly documented because that information is classified.

Both sides agree that disposing of nuclear submarines is a problem without easy solutions.

"With over 100 nuclear-powered submarines in operation, the Navy is faced with eventual decommissioning of these ships at a future rate of possibly three or four per year over the next 30 years," the Navy reported in an environmental impact notice printed in the Jan. 14 Federal Register. "A permanent means of disposal must be developed that is environmentally acceptable."

In the middle of the dispute is the Environmental Protection Agency, which must grant the Navy a permit before it can sink or bury anything that has the slightest radioactivity. The EPA's referee is senior staff oceanographer Robert Dyer. He probably is the most knowledgeable person in the country on both the science and politics of the dumping issue.

"I've conducted six hearings and all the surveys and faced all the hostile audiences," says Dyer, who has earned respect from both sides in the fight, according to environmentalists and Navy officials. "I'm in the middle somewhere and trying to stay there. But it gets tougher all the time."

The fight over submarine disposal is expected to be particularly intense because it comes at a time when the EPA is drafting new guidelines on ocean dumping. Environmentalists are hoping for a moratorium on all dumping. But last year a presidential advisory committee on oceans and atmospheres concluded that the oceans were being underutilized for dumping.

The decision on the submarines, which might not be made for a year or more, could significantly influence how the more serious problem of overall high-level nuclear waste disposal is decided. In 1980 there were about 80 million gallons of high-level wastes and 12,000 tons of spent nuclear fuel rods in temporary storage in the United States. There have been proposals to bury the waste in abandoned caves or in natural salt domes. Two years ago the Department of Energy spent $5.9 million to study a plan to "rocket" the waste hundreds of feet into the ocean floor.

Before the United States suspended offshore dumping of nuclear waste in 1970, thousands of gallons of low-level wastes were dumped into both the Atlantic and Pacific oceans. In 1975 the EPA reported traces of radioactive leaks from containers 120 miles east of Ocean City, Md. Musick has caught two fish off the Maryland shore that showed significant levels of radioactivity.

"There is definitely a threat to commercial fishing," says Jon Hinck, an official with Greenpeace, an international environmental activist group. "But the greater implication is of reversing recent U.S. policy on nuclear dumping at sea."

Hinck is afraid that if the United States relaxes its rules on nuclear waste dumping, it will encourage other countries such as Great Britain and France to do the same.

But the EPA's Dyer says that if the Navy shows the radiation levels from its submarines are within limits set by the 1972 Ocean Dumping Treaty, which was ratified by the United States, his agency will have little choice but to grant a permit.

"You can guess almost every environmental lobby group will not like it and the public will not like it," says Dyer, who adds his agency will be obliged to make its decision primarily on data alone. "They will give me 100 reasons of an emotional nature against it. But from the preliminary numbers I have seen, in no way shape or form will (the submarines) exceed those definitions."