The National Weather Service has confirmed that two tornadoes, one in Mayport and another in Fernandina Beach, touched down late Thursday afternoon.
Waterspouts moved along the coast of northeast Florida, eventually making landfall.
Naval Station Mayport saw wind damage to the roof of one building and tables tossed into the windows of another.
Navy public affairs officer Chief William Townsend reported the damage to some buildings on the base was minor. He said no funnel cloud touched the ground at Mayport, but there was wind and rain damage. There were no injuries reported.
IMAGES: Damage from twisters along coast
The National Weather Service issued a tornado warning about 4:45 p.m. for northeast Duval County and southeast Nassau County. About 20 minutes later, Channel 4 got reports of storm damage on the base.
Fernandina Beach police a water spout knocked down trees and power lines and caused roof damage to one home along South Fletcher Avenue between Jasmine Street and Atlantic Avenue.
Just a few minutes after the storm blew through the beach town, homeowners headed outside to survey the damage and start cleaning up.
A pile of lumber that lay on the streets of Fernandina Beach became a pile of lumber after the wood blew off the back of a nearby home. When the storm was at its worse, Mike Ivey, who has been vacationing in Fernandina Beach, put his family into survival mode and moved them to the safest part of their rental home.
"I've always heard, get in an interior room, so that's what we did," said Ivey. "Even broke sheetrock in bathroom area where this hit on the side of the house."
"If we looked at dunes, we could see the tornado going that way, then we came out and saw this, but it was so close to us," said Liam Carroll.
Carroll and his mom said they saw the tornado after it hit their town.
"As soon as I put the phone down with his dad, there was a huge gush of wind," said Alexandra Carroll. "I looked out it was literally coming off the ocean and I got so frightened, told him, 'Run!'"
Carroll and her son ran into the closed and waited until they said it sounded safe. They said the sounds they heard will never leave them.
"It was so fast! It was one minute calm, then all of a sudden whoosh!" said Carroll. "Everything was everywhere. Obviously, you've seen the damage."
"My mom was frightened. I was chill at the time, but I got scared," said Liam Carroll.
Several roads were also blocked by downed trees. No injuries were reported.
Chief Meteorologist John Gaughan says a second waterspout formed off the coast of St. Marys, Ga., about 5:15 p.m.
"The rotating squall line is hugging the coast, moving north," Gaughan said on the air just after 5:30 p.m. "The tornado warning was just extended north to Glynn County."