“The worst thing about a bridge, any bridge, is what it has in common with all man-made structures,” he wrote. “It is a land-killer, a dead footprint on land or water. To last for centuries, to provide a sheltered roadway, to serve all creatures and to present a living surface to the sky, a bridge must have a roof and a deep covering of earth.”

Mr. Wells never saw his ideas take root, so to speak, and catalyze the vast change in building standards that he advocated, but his ideas influenced architects that came after him, especially in the 1970s, as the environmental movement gained traction. The New York Times estimated in 1979 that underground houses, virtually nonexistent at the start of the decade, would number as many as 2,000 by the end.

“As a thinker, he was a hidden jewel,” said William McDonough, an architect and the author, with Michael Braungart, of “Cradle to Cradle: Remaking the Way We Make Things,” an environmental-design manifesto.

“In the world of what has become known as green building,” Mr. McDonough added, “Malcolm Wells was seminal, actually inspirational, for some people, me included.”

Malcolm Bramley Wells was born in Camden, N.J., on March 11, 1926, and grew up in nearby Haddonfield. After high school, he joined the Marines and was sent for a time to Georgia Tech, where he studied engineering. He later took courses at Drexel Institute of Technology, now Drexel University, in Philadelphia, but he never received a degree.

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Mr. Wells earned a living as a draftsman and went to work for RCA, starting by drawing designs for portable radios and eventually remodeling showrooms. He apprenticed at a small architectural firm in New Jersey until he passed the state exam, becoming an architect in 1953. He had commissions in the United States and abroad; eventually he designed the RCA pavilion at the 1964 World’s Fair in New York City.

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It was at this point that he abruptly changed course. With the realization that the pavilion would be torn down two years after it was completed and that all his other buildings, with their parking lots and concrete footprints, had destroyed whatever had lived there before them, he began to develop his theories of gentle architecture. He was influenced by the nascent environmental movement, by Taliesin West, Frank Lloyd Wright’s low-slung desert house and studio in Scottsdale, Ariz., and by the work of a French architect, Jacque Couëlle.

Mr. Wells, who wrote a number of books, including “Gentle Architecture” (1981), “Infra Structures” (1994) and “Recovering America” (1999), taught environmental design at Harvard in the mid-1970s and lectured at other architecture schools through the ’80s.

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He also lived his philosophy, building underground homes and offices for himself, first in New Jersey and later on Cape Cod. He bicycled to work.

His first marriage, to Shirley Holmes, ended in divorce. In addition to his son Sam, an architect who lives in Petaluma, Calif., he is survived by his wife, Karen North Wells; a daughter, Kappy Wells, of Santa Fe, N.M.; another son, John, of Harleysville, Pa.; a stepson, Jonathan Kelly, of Wellfleet, Mass.; a stepdaughter, Kirsten Engstrom, of Bedford, N.H., and seven grandchildren.

“I’m a lucky man,” Mr. Wells, in declining health, wrote in 2006 in an attempt at his own obituary. He added: “I am an atheist, a Democrat, a skinny old bearded guy, and an owner, with Karen, of the Underground Art Gallery at 673 Satucket Road in Brewster. My former wife, Shirley, down in Cherry Hill, N.J., remained and is a better person and better sport than I would have been if she’d left me. (My luck continues.)”