The skulls, some of which are as much as 10,000 years old, were found on a sand bar near Pierre, the Rapid City (S.D.) Journal reported Saturday.
Archaeologists from the Archaeological Research Center in Rapid City and the South Dakota School of Mines and Technology will travel to the site to search for more bones and fossils.
"We're going to go out to the area where they were collected and see if we can identify other species that are relatively uncommon -- specifically Ice Age mammals, like ground sloth, camel [and] horse," said assistant state archaeologist Michael Fosha.
It is unclear why all of the skulls washed up in one place, but it is possible the location was a natural gathering spot for bison or a village or hunting ground, Fosha said.
The skull collection will be displayed in Rapid City museums and will ultimately be divided between the Archaeological Research Center and the School of Mines' respective museums.