Carlo Nicholson, who has never drunk alcohol, said a large bottle of cider was poured onto a towel over face by other Marines.
The waterboarding was part of a series of tasks and punishments which formed an initiation ceremony into 45 Commando, based at Royal Marine Condor, Arbroath.
Portsmouth Military Court, Hants, heard Mr Nicholson and other new recruits were made to fight while naked and covered in cooking oil and eat dog food out of a mess tin.
Other tasks included lying in a pool of urine and vomit.
Former marine Ryan Logan is accused of ‘reefing’ Mr Nicholson - striking him with a leather belt when he failed a task and also of waterboarding him.
The court heard, Mr Nicholson, who joined the marines in January 2014, had spoken to someone about possibly leaving before the initiation on 7 May 2014.
Mr Nicholson left 45 Commando in December 2014 and told the court the initiation ceremony “destroyed” his dreams of a military career.
Fiona Edington, defending Ryan Logan, said: “To confirm you say he hit you with a belt once, and hit you with a new implement three times.
“And he had the bottles of cider when you were waterboarded.”
Mr Nicholson replied: “Yes, of course. I first saw the bottles when the towel was removed and Logan was holding them.”
Marine Ian Tennet, 32, is also accused of the ill-treatment of a subordinate, while ex-Marine Logan, 25, faces trial for battery and disgraceful conduct of a cruel kind.
The court heard a total of 26 new recruits took part in the initiation ceremony which some described as a bonding exercise.
When asked if he had been aware of the joining run being a marine tradition, Marine Anthony Murphy told the court: “Yes, it was.”
Marine Kane Hyett said after the initiation he felt closer to his colleagues.
He said: “I wanted to do it. Before the joining run I was getting ready, setting up, getting the kit ready.”
The trial continues.