Geer was born in Frankfort, Indiana, where he was deeply influenced by his grandfather, who taught him the botanical names of the plants in his native state. Geer started out to become a botanist, studying the subject and obtaining a master's degree at the University of Chicago. While at Chicago he also became a member of Lambda Chi Alpha Fraternity.
He began his acting career touring in tent shows and on river boats. He worked on several left-oriented documentaries, including narrating Sheldon Dick's Men and Dust, about silicosis among miners.
Geer was also the lover of gay activist Harry Hay In 1934, Hay met Geer at the Tony Pastor Theatre, where Geer worked as an actor. They became lovers, and Hay credited as his political mentor. Hay and Geer participated in a milk strike in Los Angeles, where Hay was first exposed to radical gay activism in the person of "Clarabelle," a drag queen who held court in the Bunker Hill neighborhood, who hid Hay from police. Later that year, Hay and Geer performed in support of the San Francisco General Strike.
Geer made his Broadway debut as Pistol in a 1928 production of Much Ado About Nothing, created the role of Mr. Mister in Marc Blitzstein's The Cradle Will Rock, played Candy in John Steinbeck's theatrical adaptation of his novella Of Mice and Men, and appeared in numerous plays and revues throughout the 1940s. From 1948 to 1951, he appeared in more than a dozen movies, including Winchester '73, Broken Arrow, and Bright Victory.
Geer became a member of the Communist Party of the United States in 1934. Geer was also influential in introducing Harry Hay to organizing in the Communist Party. In 1934, Geer and Hay gave support to a labor strike of the port of San Francisco; the 1934 West Coast waterfront strike lasted 83 days. Though marred by violence, it was an organizing triumph, one that became a model for future union strikes. Geer became a reader of the West Coast Communist newspaper, the People's World.
Geer became a dedicated activist, touring government work camps in the 1930s with folk singers like Burl Ives and Woody Guthrie (whom he introduced to the People's World and the Daily Worker; Guthrie would go on to write a column for the latter paper). In 1956, the duo released an album together on Folkways Records, titled Bound for Glory: Songs and Stories of Woody Guthrie. In his autobiography, fellow organizer and gay rights pioneer Harry Hay described Geer's activism and outlined their relationship while organizing for the strike. Geer is credited with introducing Guthrie to Pete Seeger at the 'Grapes of Wrath' benefit Geer organized in 1940 for migrant farm workers.
Geer did summer stock at the Pine Brook Country Club located in the countryside of Nichols, Connecticut with the Group Theatre (New York) studying under Harold Clurman, Cheryl Crawford and Lee Strasberg. The artists took up residency at the lake in summer from 1931 until the early 1940s.
Geer was blacklisted in the early 1950s for refusing to testify before the House Committee on Un-American Activities. During that period, he built the Will Geer Theatricum Botanicum in Topanga, California, which he and his companion, Herta Ware, helped to found. He combined his acting and botanical careers at the Theatricum, by making sure that every plant mentioned in Shakespeare was grown there.
In the late 1950s and early 1960s he played several seasons at the American Shakespeare Festival in Stratford, Connecticut, where he created a second "Shakespeare Garden" on the theater's grounds. By this time he was also working sporadically on Broadway. In 1964 he was nominated for the Tony Award for Best Featured Actor in a Musical for 110 in the Shade. In 1972, he played the part of "Bear Claw" in Jeremiah Johnson along with Robert Redford.
Geer maintained a garden at his vacation home, called Geer-Gore Gardens, in Nichols, Connecticut. He visited often and attended the local Fourth of July fireworks celebrations, sometimes wearing a black top hat or straw hat and always his trademark denim overalls with only one suspender hooked.
When Geer died, shortly after completing the sixth season of The Waltons, the death of his character was written into the show's script as well.
His ex-wife, actress Herta Ware, was best known for her performance as the wife of Jack Gilford in the film Cocoon (1985). Although they eventually divorced, they remained close throughout the rest of their lives. Geer and Ware had three children, Kate Geer, Thad Geer and actress Ellen Geer. Ware also had a daughter, actress Melora Marshall, from a previous marriage.