GUANTÁNAMO BAY, Cuba — A Saudi defendant in the destroyer Cole bombing case who was subjected to waterboarding and a mock execution by the C.I.A. in 2002 still has nightmares of drowning, sleeps with a light on in his cell and can shower only in a trickle of water, a doctor who specializes in treating torture victims testified on Tuesday.

When he has been driven to court in a standard windowless detainee transport van, the defendant, Abd al-Rahim al-Nashiri, 56, also gets nauseous and vomits from flashbacks to a period when agents confined him nude and shivering inside a chilled, cramped box, part of the “enhanced interrogation” program at the agency’s secret sites.

Defense lawyers elicited the testimony from Dr. Sondra S. Crosby, a Boston internist who has been evaluating and treating torture victims since the 1990s. Mr. Nashiri is accused of being the mastermind of the suicide bombing of the ship off Aden, Yemen, in October 2000 that killed 17 U.S. sailors.

His lawyers are seeking a court order to let him spend the night before a hearing at a specially equipped holding cell at the court, as a disabled prisoner in another case has done. The trip from prison to court, they argue, is traumatic and interferes with his ability to concentrate on the death-penalty proceedings and cooperate with his defense team of Navy and civilian lawyers.

The testimony highlighted how Guantánamo Bay, a Pentagon operation that turns 20 on Jan. 11, still has no formal program for providing care to torture victims. Dr. Crosby was testifying as a Pentagon-paid consultant to the defense team, a role she has held since 2012.

Mr. Nashiri “was subjected to many horrific torture methods while he was in the black sites,” the doctor said. His time in the “small box,” she said, was “really distressing and horrible” because it was done repeatedly.

Dr. Crosby said Mr. Nashiri had irritable bowel syndrome, which is not unusual for a rape victim or someone with post-traumatic stress disorder. She cited once-classified records that showed that Mr. Nashiri, while held by the C.I.A., was sodomized with a brush and, separately, through a procedure she cast as bogus to “rectally feed him,” was raped with “an object.” Another detainee recently described that object as a garden hose.

In 2013, a military board made up of three Army officers, one psychiatrist and two psychologists, diagnosed Mr. Nashiri with PTSD and depression, and also called him an antisocial narcissist.

A prosecutor, Lt. Cmdr. Cherie Jolly of the Navy, suggested on Tuesday that Mr. Nashiri’s psychological and health problems predated his capture in Dubai in October 2002. She attributed a tear in the prisoner’s rectum to a poor diet and constipation in his youth.

She also suggested that traumatic brain injury discovered on an M.R.I. of Mr. Nashiri at Guantánamo was the result of his role as “a battlefield participant” with Osama bin Laden, rather than Dr. Crosby’s explanation that he was repeatedly punched in the head while in C.I.A. custody, and for a time lost his hearing.

One of Mr. Nashiri’s defense lawyers, Annie W. Morgan, who is a Defense Department employee, described Tuesday’s testimony as the first open-court airing in detail of some of the torture he underwent as a C.I.A. prisoner, both in Afghanistan and at a secret site in Thailand.

Mr. Nashiri knew in advance what would be discussed, and “wants people to know what America did to him,” Ms. Morgan said. Still, because of the material, she said, he voluntarily stayed away from the courtroom during his team’s “first chance in an unclassified setting to tell his story.”

His nausea on trips to court has been a source of dispute since before the coronavirus pandemic stalled proceedings. Military doctors have cast it as run-of-the-mill motion sickness. Dr. Crosby said it was triggered by memories of the confinement box when Mr. Nashiri was transported in a windowless van. It affects him less so, she said, when the prison staff members are “kind” and transport him to court in a small school bus with the windows uncovered.

To go to court, prison doctors have been giving Mr. Nashiri both an antihistamine, Meclizine, which makes him sleepy, and Adderall, to perk him up. On questioning from the prosecutor, Dr. Crosby said she would like to discuss the unusual combination with his prison doctor, the latest in a series of Navy officers on temporary assignment to the detention operation.

The prosecutor noted that, in court, Mr. Nashiri sometimes appeared to swagger. At his first court appearance in November 2011, he turned and waved toward the gallery, where reporters and family members of victims of the Cole attack were watching.

But Dr. Crosby said that he was frequently fearful of both real and imagined things, and cited examples. He is afraid that a tsunami or a hurricane will hit the base in southeast Cuba and that his guards will abandon him in his cell to drown. He also reported being assaulted by another former C.I.A. prisoner this year, which has left him “hypervigilant and frightened that something might happen to him.”

As Dr. Crosby was expanding on the episode, a court security officer pushed a mute button, replacing audio to the public with white noise, suggesting that the testimony strayed into classified information. The censorship episode was brief, and the court was back in open session within minutes.