Dr. Herbert Pardes, a psychiatrist and a former director of the National Institute of Mental Health who brought order to the merger of two major medical centers that became New York-Presbyterian Hospital and ran it for 11 years, died on April 30 at his home in Manhattan. He was 89.

His son Steve said the cause was aortic stenosis.

Dr. Pardes (pronounced par-diss) was named president and chief executive of the hospital in late 1999, nearly two years after the merger of New York Hospital and Presbyterian Hospital. The previous decade, he had been the dean of the faculty of medicine at the Columbia University College of Physicians and Surgeons, Presbyterian’s affiliated medical school.

“It was no secret that as dean of the medical school I didn’t always agree with the hospital administration,” he said in his thick Bronx accent on CUNY TV in 2011. “I thought maybe I could create a better collaboration by going over to run the hospital.”

The merger created one of the largest health care institutions in the country, with 2,369 hospital beds, 13,000 employees and $1.6 billion in annual revenue. With 167 facilities, it spread from Manhattan to Rockland and Orange Counties in New York. Its hospitals include the Weill Cornell Medical Center in Manhattan.

“It was an amazingly accomplished merger considering the different cultures of the two institutions,” Kenneth E. Raske, president of the Greater New York Hospital Association, a trade group, said in an interview. “He was the bridge that allowed the smooth and wrinkle-free transition of that institution.”

But Alan Sager, a professor of health law at Boston University, without commenting on the New York-Presbyterian merger, said in an email, “Proponents of mergers always say, in a self-sanctifying way, that they are combining to help us, not themselves. But if mergers did cut costs (never substantiated), heftier hospital surpluses would result — not lower insurance premiums.”

Dr. Pardes aspired to make New York-Presbyterian a model for medical care, with intense focus on patients, efficient management and rigid financial controls. He visited bedsides, insisted that nurses memorize patients’ and their families’ names, and ordered rooms and lobbies to be painted in soothing colors.

“I’ve never been able to walk past a problem,” he was quoted as saying in a profile about him in The New York Times in 2007. “I’ve got to fix it. This profession is first about helping patients survive — always has been. Unfortunately, I think we can lose sight of that sometimes.”

Mr. Raske said, “Herb met life’s problems with a childlike grin and a touch of borscht belt humor.”

Dr. Pardes was a prodigious fund-raiser for New York-Presbyterian, helping to secure donations from the megawealthy to build facilities like the Morgan Stanley Children’s Hospital, the Vivian and Seymour Milstein Family Heart Center, and the Iris Cantor Men’s and Women’s Health Centers, all in Manhattan.

“He had a way of socializing with high-powered people and talking them into making huge gifts,” Steve Pardes said.

Herbert Pardes was born on July 7, 1934, in the Bronx and grew up mainly in Lakewood, N.J. His parents, Louis and Frances (Bergman) Pardes, owned the Hotel Greenwood in Lakewood, which was converted into a nursing home in the late 1950s, and managed resorts in the borscht belt of the Catskills.

At 7, Herbert was diagnosed with Perthes disease, a rare childhood illness in which the blood supply to the ball part of the hip joint is temporarily interrupted, weakening the bone. Though he recovered without any lasting damage, he spent 10 months hospitalized in a full-body cast. Grim physicians stuck needles in him without explanation, and hospital rules limited his parents’ visits to just an hour a couple of times a week, he recalled. The experience traumatized him but, decades later, helped motivate him to be more attentive to patients.

As a youth he worked for his parents, observing how they pampered resort guests. He sold sodas for 10 cents, raised money for the war effort, bell-hopped, waited tables and rose to maître d’hôtel.

“The dining room was a microcosm of eccentric behavior, a great behavior lab for someone who would develop into a psychiatrist,” Dr. Pardes told The Times in 2003.

He graduated from Rutgers University in 1956 with a bachelor’s degree, then earned his medical degree in 1960 from SUNY Downstate College of Medicine (now SUNY Downstate Health Sciences University) in Brooklyn. He served his medical internship and psychiatric residency at Kings County County Hospital in Brooklyn from 1960 to 1962.

After being drafted into the Army, Dr. Pardes ran the mental hygiene clinic at Fort Myer in Arlington, Va., from 1962 to 1964. He was discharged and completed his residency in 1966, then graduated from the New York Psychoanalytic Institute in 1970.

For most of the next two decades he built his career around mental health as chairman of the department of psychiatry at Downstate, chairman of the psychiatry department at the University of Colorado Medical Center in Denver, and director of the N.I.M.H., where he strengthened its research program.

In 1984, Dr. Pardes was appointed director of psychiatry service at Columbia University Irving Medical Center and chairman of the psychiatry department at the College of Physicians and Surgeons. Five years later, he was named the college’s vice president for health sciences and dean of the faculty of medicine, positioning him to run New York-Presbyterian Hospital after the merger.

In addition to his son Steve, he is survived by two other sons, James and Lawrence, six grandchildren and his partner, Dr. Nancy Wexler, a professor of neuropsychology at the College of Physicians and Surgeons who was the lead researcher for a study of an extended family’s Huntington’s disease in Venezuela for two decades. She herself has the disease. He had been separated from his wife, Judith (Silber) Pardes, since the 1980s. She died in 2022.

Dr. Pardes was a well-paid nonprofit executive, even after he stepped down as president and chief executive in 2011. He was subsequently named executive vice chairman of the hospital’s board of trustees, a position that compensation experts said was rare in the nonprofit world, according to an article in The Times in 2014.

In 2011, his final year running the hospital, he earned $4.1 million (equivalent to about $5.8 million today). Then, as executive vice chairman, he received, $5.5 million, including $2 million in deferred compensation in 2012. Through 2022, he received at least $2 million annually.

Frank Bennack Jr., then the hospital’s board chairman, told The Times in a statement in 2014 that Dr. Pardes had been retained for “urgent fund-raising activities and a range of other institutional needs with which he could assist his superb successor.”

Dr. Steven J. Corwin succeeded him and remains in that position.

Steve Pardes said the focus on compensation annoyed his father. “When he compared himself to C.E.O.’s in profitable businesses, he might have been undercompensated,” Mr. Pardes said. “But he wasn’t money-focused. He wanted to be paid a fair wage for what he contributed.”