By placing the ship – La Belle – in a constant environment of up to 60 degrees below zero, more than 300 years of moisture will be safely removed from hundreds of European oak and pine timbers and planks.
The freeze-dryer, located at the old Bryan Air Force base several miles northwest of College Station, is 40 feet long and 8 feet wide – the biggest such machine on the continent devoted to archaeology.
Researchers will then rebuild the 54 ½-foot vessel, which will become the centrepiece of the Bob Bullock Texas State History Museum in Austin.
From a historical perspective, it's "an icon of a small event that dramatically changed the course of Texas history," said Jim Bruseth, who led the Texas Historical Commission effort to recover the remains.
The ship was built in 1684 and sank two years later in a storm on Matagorda Bay, about midway between Galveston and Corpus Christi. Captained by Rene-Robert Cavelier Sieur de La Salle, he hoped to colonise Texas for France.
"When La Belle sank, that doomed La Salle's colony and opened up the door for Spain to come in and occupy Texas," Mr Bruseth said. "People can see firsthand how history can turn on a dime."
Researchers have determined that unlike earlier vessels, the frames on La Belle were marked specifically by the French craftsmen so the wood comprising the hull could follow the complex curve of the ship.
After a more than decade-long hunt, Texas Historical Commission archaeologists found it in 1995 in 12 feet of murky water. Then began the tedious recovery that involved constructing a dam around the site.