The 23-year-old man from Ruskin, Florida, was arrested Monday on a charge of felony aggravated animal cruelty.
A case docket hadn't yet been posted online so it was unknown if he had an attorney.
The dog, nicknamed Trooper by the Florida Highway Patrol, was found alive last Wednesday in floodwaters up to his chest along Interstate 75 in the Tampa area as residents evacuated Florida's Gulf Coast hours before the Category 3 hurricane made landfall.
Troopers brought him to a vet, where he was examined for injuries and received a clean bill of health.
"We take this crime very seriously and this defendant will face the consequences of his actions," said State Attorney Suzy Lopez, whose jurisdiction covers the Tampa area.
A trooper who located the dog based on a description from a witness driving by described him as "in severe distress and trembling," according to a redacted criminal report.
"Traffic was heavy as many people were evacuating," the trooper wrote in the arrest report. "Due to the circumstances, and the extreme danger and risk of death caused by the defendant to the dog, the defendant's actions caused excessive unnecessary infliction of pain and suffering to the dog."
Investigators were able to track down the owner after he went to a Tampa area animal shelter looking for his dog, who had been moved to a shelter in Tallahassee and then placed with a foster family. The owner agreed to give up the dog to the foster family provided "they would take good care and love the dog," the arrest report said.
During an interview with the trooper, the owner waived his right to remain silent and gave a statement which was redacted in the report.