Three children were injured, according to local news reports, as the castle was flipped over and launched upward - but all three were thrown from the castle at a low height.
A video posted to Facebook by beachgoer Brandon Burchett showed the incident, beginning as he began recording the whipped-up spray on the water's surface.
The US National Weather Service said it was an EF-0 tornado - the lowest classification - with en estimated wind speed of a little over 100kph.
The bouncy castle was picked up over a car parking area and flung across several lanes of traffic.
NBC Miami said the children were recovering in hospital following the incident.
"I was in the bounce house and a tornado while I was in the bounce house and I flew up and dropped," six-year-old Shamoya Ferguson said.
Shadaja Bryant, aged five, broke her arm in the incident, and later said "I was thinking I was about to die."
"I was in the bounce house and then it flew while I was in there, then I fell in the dirt."
The tornado did only minor damage to the area, and one of the children was kept in hospital for observation.