Deschanel was born in Philadelphia, Pennsylvania, the son of Ann Ward (née Orr) and Paul Jules Deschanel. His father was French, from Oullins, Rhône, and his mother was a United States citizen. Deschanel was raised in his mother's Quaker religion.
He enrolled in Severn School for his high school years. He attended Johns Hopkins University from 1962 to 1966, where he met Walter Murch, with whom he staged "happenings," including a memorable one in which Murch simply sat down and ate an apple for an audience. Murch graduated a year ahead of him and encouraged Deschanel to follow him to the University of Southern California School of Cinematic Arts, where he graduated in 1968. During this time, Deschanel was a member of a band of film students called "The Dirty Dozen;" this group attracted attention from the Hollywood system. Following his graduation, he attended the American Film Institute (AFI) Conservatory and graduated in 1969 as a member of its first class.
Deschanel joined the American Society of Cinematographers, or A.S.C., in 1969, the year of his graduation from the AFI Conservatory. In 1972, three years later, he married the former Mary Jo Weir. The older of their two daughters, Emily, was born in 1976; their younger daughter, Zooey, was born in 1980.
Deschanel's cinematography credits include: A Woman Under the Influence (1974, John Cassavetes directing), Being There (1979, Hal Ashby directing), The Black Stallion (1979), The Right Stuff (1983), The Natural (1984), Fly Away Home (1996), The Patriot (2000), Timeline (2003), and The Passion of the Christ (2004, Mel Gibson directing).
Like many cinematographers, Deschanel has also directed feature films and television series episodes. He directed his first film, The Escape Artist, in 1982, and a second, Crusoe, in 1989. In 1990, Deschanel directed three episodes of the David Lynch series Twin Peaks. In 2007, he directed an episode of Bones, which starred his daughter Emily as Dr. Temperance Brennan. He was the cinematographer in the 2009 film My Sister's Keeper, and also the cinematographer for the 2011 thriller Dream House.
He was an original member of the American Zoetrope production team, along with George Lucas and Francis Ford Coppola.
Deschanel was awarded the ASC Lifetime Achievement Award in 2010 by the American Society of Cinematographers.
He has been nominated for five Academy Awards, each time in the field of cinematography. The first nomination came in 1983 for the film The Right Stuff. His second was in 1984 for The Natural. A third came in 1996 for Fly Away Home, then a fourth in 2000 for The Patriot, and finally a fifth for his work in The Passion of the Christ. But he lost to other cinematographers all five times.
Another award Deschanel did win was the American Society of Cinematographers (ASC) award, which was for his work in The Patriot.The Escape Artist (1982)
As of the middle of June 2017, Deschanel was also involved in the then in-production live-action film version of The Lion King, based on the 1994 feature-length animated cartoon, which was slated for release in 2019.