The fish were first spotted by beachgoers taking advantage of the unseasonably warm weather.
"We came down to the beach for the day just to have, you know, a nice day on the beach, smell the fish smell, came down to look for shells and all these fish -- dead," Pat Hawkins, a Pawleys Island resident told NBC station WMBF in Myrtle Beach, S.C. "It's a shame. I don't know what's causing it."
Officials from the Department of Health and Environmental Control and the Department of Natural Resources visited the area Tuesday and took water samples in an effort to determine what killed the fish.
Marine experts determined the fish died from hypoxia, which occurs when the amount of oxygen in the water drops.
Mel Bell, director of the Office of Fisheries Management for the South Carolina Department of Natural Resources, said the occurrence was an entirely natural event.
"On Friday we had a new moon (which caused) real high high tides and real low low tides," Bell told The Sun News. "Probably what happened was a school (of menhaden) got in an area of water on a high tide, in a hole or depression, and at low tide they were trapped and depleted the oxygen in the water. Then, all the fish would suffocate. Then, when the tide came back in, it washed the dead fish out and they washed up on the beach."
"When it's one species like that, that's usually indicative of a low dissolved oxygen situation because they tend to be more fragile," added Dan Hitchcock, an assistant professor at the Baruch Institute of Coastal Ecology and Forest Science at Clemson University in Georgetown, S.C.
Fanning said the city has no plans to clean up the fish and will let the seagulls and the tide clear the sand.
"We're just dealing with it as a force of nature," Fanning said. "There are some residual fish (on Thursday), most of it has gotten washed away, there were a ton of birds down there. If you went down there today, you'd get more birds than fish."
Menhaden fish, typically used by fishermen as bait, are a small, silver fish, whose oil is used in vitamin supplements, lipstick and livestock feed.