No injuries have been reported as a result of the blaze that broke out about 2:30 p.m.Monday.
An estimated 40 firefighters were on the scene of the blaze, which was producing thick black smoke visible for miles, said Candice Temple, county spokeswoman.
"The fire is contained to the two rail cars and the trestle right now," Temple said.
The trestle is in the middle of marsh, making it difficult for firefighters to reach, she said.
"The fire is burning so hot that it has warped the steel rails preventing firefighters and ports authorities crews from unhooking the burning cars from the rest of the freight train, Temple said.
Traffic on neighboring Interstate 95 and U.S. 17 is moving smoothly. The wind is blowing the smoke away from U.S. 17, she said.
The same trestle burned about five years ago, hampering port operations at the shipping terminal which handles a variety of cargo including motor vehicles and heavy equipment.