Navy Capt. John R. Nettleton remains on active duty, but he was removed from command shortly after civilian Christopher Tur was found floating in January 2015 in the waters off the base on the southeastern coast of Cuba.
Nettleton was accused in a federal indictment of obstruction of justice and concealing material facts, including that he and Tur had brawled, in an alcohol-fueled encounter at a base nightclub, after Tur accused the commander of having the affair.
Nettleton denied to his superior officer and others that he had the affair, but investigators later determined that it had happened, according to an indictment issued in Jacksonville, Florida, where Nettleton has been on temporary duty.
Tur's older brother, Michael, welcomed the indictment. Nettleton is "facing some serious felony charges," he said. "It's not a homicide charge, but he's facing some serious jail time."
Nettleton was commander of the base since June 2012, but not the detention center where suspected terrorists are held.
An autopsy found that Tur, 42, died from drowning but that he had broken ribs suffered before he went into the water and a cut to his head. The investigation also turned up blood from Tur inside the entryway of Nettleton's residence on the base and from a paper towel in the backyard.
Tur came to Guantanamo in May 2011 with his wife, Lara, and two children and worked as the loss prevention safety manager at the Navy Exchange, the main shopping complex on the base.
On the night of his disappearance, Tur confronted the commander and Tur's wife in front of witnesses at a party at the on-base nightclub. Each had "consumed several alcoholic drinks," according to the indictment.
Tur later that night went to Nettleton's residence, where the two men fought. Nettleton's daughter heard the commotion and came down to see her father on the ground and Tur standing over him with a telephone shortly before he left the area and wasn't seen again.
Around that time, a friend of Tur's reported getting a call from him in which Tur said he was at Nettleton's house and had "just knocked the skipper out."
The indictment said Nettleton repeatedly misled officials during the search for Tur and later encouraged Lara Tur to deny their affair to investigators. The document doesn't say how authorities later confirmed the affair.
Nettleton, 53, was arraigned Wednesday in Jacksonville on charges of obstruction of justice, concealment, falsifying records and making false statements to investigators. A plea of not guilty was entered on his behalf and he was released on bond.
Colby Vokey, a lawyer for the Navy officer, declined comment.