The toddler was reported missing on June 16 by her cousin, 18-year-old Engelica Castillo, who had been taking care of the child since June 8.
Castillo and 24-year-old Tim Tkachik, both of Hobart, Ind., were charged with murder, neglect of a dependent, battery and false informing. Each faces a sentence of 45 to 65 years if convicted of the killing.
They were being held without bond Friday in the Lake County Jail.
According to court documents, an autopsy showed Jada had numerous skull fractures.
"This tragic ending is not the outcome we were all hoping for," said Lake County prosecutor Bernard Carter.
The affidavit gives details of an elaborate attempt to cover up the child's apparent beating death.
Castillo had claimed that Jada disappeared from a car while the teenager went into a convenience store in Gary. The affidavit says Tkachik told police that Castillo had beaten the child severely on the head on June 13 after they had both used heroin, and they noticed Jada wasn't breathing when they drove to buy more heroin that evening.
"I told you to stop. I told you enough is enough," Tkachik said he told Castillo, according to the affidavit. The pair allegedly repeatedly tried CPR to revive the child.
According to the affidavit, the pair took Jada home and, thinking she was still breathing, took her into the house. Once they realized she was dead, the document says, they decided to get rid of the body.
Tkachik allegedly put the body in garbage bags the next day and took it to a wooded area in LaPorte County, where he tried unsuccessfully to burn it, causing an explosion that burned his face and required hospital treatment. Tkachik blamed the burns on a propane grill, police said.
Castillo and Tkachik then took the body home again, the affidavit said, and on June 15 entombed the remains in a tub full of concrete. After the concrete dried, the pair took the toddler's body to a rural area near Westville and sank it in a swamp, according to the document.
On Thursday, Tkachik led police to the area where the body was hidden and FBI agents recovered the remains that were later identified as Jada's, the affidavit said.
Police and the FBI took part in the 10-day search, and the FBI opened a hot line that received more than 100 tips.
According to the affidavit, Castillo told police that she routinely took care of the toddler for days and was scheduled to return the girl to her parents on June 20.
Castillo's attorney, T. Edward Page of Merrillville, did not return a phone message seeking comment Friday. Tkachik did not yet have a lawyer.