The teens were arrested Sunday after the Grand County Sheriff's Office received information about the disappearance of Gregorio Salazar Campos, who had been reported missing on March 29.
Campos' body was found and retrieved from the Colorado River on Sunday, the sheriff's office said in a news release. Campos suffered multiple gunshot wounds, the sheriff's office said.
An official cause of death is pending an autopsy by the state medical examiner.
It was not immediately clear whether police have recovered any firearms related to the shooting.
Multiple telephone messages left for Sheriff Steven White by The Salt Lake Tribune were not returned.
Court papers filed by prosecutors indicate the crime occurred on March 25, but the documents provide no other details about the alleged murder.
Under Utah law, prosecutors can charge 16- and 17-year-olds as adults without a hearing in juvenile court.
Court records show Kruckenberg and Nelson are scheduled for an initial appearance on April 23 before Judge Lyle Anderson.
A relative of Kruckenberg, who asked not to be identified, declined to comment on the allegations Monday evening.
Over the past eight years, Campos had lived off and on with his sister in a Moab mobile home park owned by Ed Nelson. Campos was hard-working construction worker who sent money from his paycheck back to family in Mexico, Nelson said.
"He was a really nice guy," said Nelson, adding that Campos' sister had asked recently if he had seen her brother. "He wasn't a trouble-causer."
Tribune reporter Janelle Stecklein contributed to this story.