The 24-year-old man was reported missing by a friend who apparently witnessed the attack at a campground along the Mary River.
"He was in shock,'' said Erin Bayard, an employee of the campground. "Two local boys decided to go swimming, we tell people to stay away from the water, but they obviously went against this."
Bayard told The (Adelaide) Advertiser the Mary River is home to a large population of crocodiles and visitors are advised to stay out of the water.
The Advertiser said police were searching for the missing swimmer Saturday evening.