Authorities said Carly, 37, was last seen on March 27, when she met Marcus Spanavello, the father of her 4-year-old daughter. He was reported missing the next day.
Investigators said Carly’s car and her purse were recovered Tuesday at a “boat overflow ramp” near the restaurant.
Spanvello was arrested in Lebanon, Tennessee, by the Tennessee Bureau of Investigation and state troops, the Santa Rosa County Sheriff’s Office said on Facebook on Saturday.
“We found his body while executing a search warrant in Alabama. It was in a barn, in a shallow grave,” Johnson told reporters.
The sheriff said police were yet to disclose where they were taken Saturday evening, but that the property was linked to Spanavello “in a roundabout way”.
Johnson said a post-mortem would be conducted in Alabama on Monday. “A tattoo confirmed his identity,” he said.
He said he personally informed Carly’s family on Sunday and was “crushed.”
“It puts them off somewhat that they know where she is now. But it’s their daughter nonetheless… daughter and sister and it’s terrible.”
Carly’s daughter was stationed with Spanvello in Birmingham, Alabama, on Wednesday. On Sunday, Johnson said he was safe and with his family.
The sheriff’s office said Spanavello is being held in Tennessee on charges of tampering with evidence, providing false information about a missing persons investigation and destruction of evidence. It was not immediately clear on Sunday morning whether he had a lawyer who would comment on his behalf.
Spanvello reportedly took Carly’s phone “and basically got rid of it,” Johnson said at a news conference on Sunday.
Asked if Spanavello cooperated with investigators, the sheriff said, “Absolutely not.”
“He was completely uncooperative, he never cooperated with us,” he said. “It’s your child’s mother and she’s missing and you’re not going to cooperate with the authorities – it’s kind of a story,” he said.
Johnson said police believe Spanavello acted alone.
The state attorney’s office said it could take about 30 days for Spanavello to return to Florida if he does not waive the extradition.
Johnson said autopsy results of any possible additional charges are pending. He said he was unaware of any previous criminal record on Spanvello.
The sheriff praised the Major Crime Unit for working on the case.
“They went over 1,500 miles in this investigation, multiple search warrants on cars, phones, homes, properties, I can’t speak enough about them enough,” he said. “We hate that Cassie has passed away but it’s good for the family to close.”
Johnson said the investigation was ongoing.
CNN’s Abby Bustin contributed to this report.