Kevin Smith, a 45-year-old welder, was arrested at his workplace on Wednesday. Police say DNA records led them to him.
Prosecutors say that Smith killed Krystal Jean Baker, 13, then left her body under a bridge.
The arrest "is a miracle from God and all the angels,'' said the girl's mother, Jeanie Escamilla, according to the Houston Daily Chronicle.
Baker was last seen storming out of her grandmothers' house in Texas City on March 5, 1996, after the two had an argument.
"She did get in a spat with her grandmother that day," said Escamilla.
"She was a teenager," she added, according to the Galveston Daily News. "She loved you one minute and hated you the next."
Later in the day, the girl made calls from a nearby tire shop asking friends and family members to come pick her up. They didn't get to her in time.
Hours later, the teen's body was found. It took authorities two weeks to identify her. During that period, the teenager was listed as missing, and Escamilla frantically handed out pictures to try to locate her daughter.
Police say they took DNA from Smith during a recent arrest on a drug charge. They ran his sample against a database of cases, and came up with a connection to the Baker case.
"He appeared calm and he appeared like he didn't have any idea we were coming to arrest him," said Capt. Brian Goetschius of the Texas City Police Department, according to ABC News.
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If convicted, Smith could face life in prison. He is currently being held in lieu of a $1 million bail. Though Smith is a Louisiana resident, police believe he previously lived in the Texas City area. They are still trying to construct a timeline to determine where and when exactly he was in Texas City.
Escamilla said that she had left the case "in the hands of God" and focused on looking after her five grandchildren.
"I wish I could wake up out of this terrible nightmare and hold my little girl in my arms again," Escamilla said, according to the Galveston Daily News. "None of this is going to bring her back."