Boaters woke up to find the small, silvery fish floating around their vessels at King Harbor Marina.
"We believe the sardines were chased in, probably by some other type of predator fish," said Sgt. Phil Keenan of the Redondo Beach Police Department.
Authorities also tested the water for oil and other contaminants.
"There are no signs of oils or chemicals or anything else in the water that shouldn't be," said Andrew Hughan of the state Department of Fish and Game.
Millions were seen dead in the harbor, but millions were still alive and being fed on by sea lions and birds.
"The water content is good," Keenan said. "There are other fish still living. It's just the sardines that died off."
Officials initially said a red tide may have been the cause of the oxygen deprivation, but Keenan said that was not the issue. Red tide is a naturally occurring bloom of toxic algae that can poison fish or starve them of oxygen, according to Staci Gabrielli, a marine coordinator for King Harbor Marina.
"What we're operating under is that there were so many sardines, and sardines consume a lot of oxygen, and there was not enough oxygen in the confined area that they were, so they died of oxygen deprivation," Keenan said. "It's like putting too many fish in a small aquarium."
It was reported that there were millions of dead fish so thick in the marina that in some places, many of the 1,400 boats could not get out of the harbor.
"I've lived in Hermosa Beach since 1963 and I've never seen anything like this," said Bill Lyle, who was surprised to see the massive amounts of belly-up fish.
Crews say they will take the dead fish to a landfill. They had thought about putting the dead fish out in the sea, but officials said it would be impossible to accomplish.
The clean up was expected to take days.
The Associated Press contributed to this report.