A former commander of the US Navy base at Guantanamo Bay has been sentenced to two years in prison for making false statements and obstructing justice in connection with the investigation into the death of a civilian at the facility in Cuba.

Retired navy captain John Nettleton, 53, was convicted in January of this year of multiple offenses related to the death of Christopher Tur.

Tur, 42, a civilian employee at the base which houses 9/11 plotters and other detainees in the US "war on terror," was found drowned in the waters off Guantanamo on January 11, 2015.

Prior to his death, Tur accused Nettleton of having an affair with his wife, according to evidence presented at trial.

The two had a confrontation at the Officers Club on the base on the night of January 9 and again at Nettleton's home later that evening.

Tur was reported missing the next day.

Nettleton, of Jacksonville, Florida, was found guilty of misleading investigators looking into Tur's death.

The former navy captain was convicted of two counts of obstruction of justice, one count of concealment of material facts, one count of falsification of records, and two counts of making false statements.

US District Judge Timothy Corrigan sentenced Nettleton to two years in prison in Florida on Thursday and one year of supervised release.

"Nettleton misled and obstructed the investigators attempting to determine what happened to Mr. Tur, and this sentence ensures that he will pay a heavy price," acting assistant attorney general Brian Rabbitt said.