John Bruggen, the park's director, told WJAX-TV that workers were getting the alligator farm ready for opening Tuesday morning when they found evidence of a break-in.
Several lamps and signs were broken, and a statue in the middle of the crocodile ponds, which can only be reached by swimming, was toppled.
Bruggen said employees found a pair of shorts and a Crocs brand rubber shoe floating in a pool and thought it might be a prank.
Staff members said they called police after finding blood. Bruggen said a lot of blood was found at the top of the zip line platform that sits over the crocodiles.
When police got to the park, employees told officers about the blood. An officer reportedly responded, "Oh, I think we've already got the perpetrator in custody. We got somebody who told us they were bitten by an alligator."
A man wearing only his boxers had been located in a nearby neighborhood. Officials said he had blood on him.
Bruggen told WJAX-TV that the officer asked the man if he'd been messing around at the St. Augustine Alligator Farm, to which the man said, "Oh, no sir, I wasn't."
The man appeared to have several bites on his foot.
He was arrested off the property and none of the park’s crocodiles were hurt, Bruggen said.
He said this is the first time in park history that someone had jumped into one of the exhibits.
He added that in surveillance video, the man appeared to be unstable. He said the man had to climb over fencing and barbed wire to get into the pit.
"I would think he's on some sort of drugs," Bruggen said. "I'm concerned about an individual who literally climbs up a wall that's meant to keep you from crocodiles and leaps over the wall into the water with them."