William Harris Stewart was born on October 18, 1966, in Des Moines, Iowa. His father played trombone, and his first and middle names honor the jazz trombonist Bill Harris. He grew up on his parents' jazz and rhythm and blues records with little live jazz to hear in Iowa, was largely self-taught, and started on drums at seven. In high school he played in a Top 40 cover band and the school orchestra, and a summer at the Stanford Jazz Workshop brought him a meeting with Dizzy Gillespie. He studied at the University of Northern Iowa in Cedar Falls, playing in its jazz and marching bands and orchestra, then transferred to William Paterson College in New Jersey, where he played in ensembles led by Rufus Reid, studied drums with Eliot Zigmund and Horacee Arnold, and took composition lessons from Dave Samuels. It was there that he met Joe Lovano, with whom he once played duets in place of a lesson when Zigmund was away.

Stewart made his first records while still in school, with saxophonist Scott Kreitzer and pianist Armen Donelian (Secrets, 1988, and The Wayfarer, recorded 1989), and recorded with pianist Franck Amsallem and Gary Peacock in 1990. After graduating in 1988 he settled in Brooklyn and built a reputation through jam sessions and word of mouth. He began playing in an organ trio with Larry Goldings and guitarist Peter Bernstein, begun in 1989 and still his longest-running group; its debut record, Intimacy of the Blues, came out in 1991. Maceo Parker heard Stewart with Goldings at a Manhattan club, hired him for 1990 and 1991, and took him on the road and onto three albums, among them Roots Revisited (1990) and Mo' Roots (1991); the association led to a stint with James Brown, who teased him that there was no funk in Iowa. In the same early years he was the regular drummer on Lee Konitz's weekly dates at the West End Gate, before his time with John Scofield.

Scofield's quartet made Stewart's name. He joined it in 1990 and stayed about five years, recording Meant to Be (1991) and What We Do (1993) for Blue Note with Lovano in the front line, then Hand Jive (1994) with Eddie Harris and Quiet (1996, Verve). Along the way he recorded his own debut as leader, Think Before You Think (recorded August 1989, issued 1990 by the Japanese label Jazz City), with Lovano, pianist Marc Copland, and Dave Holland, and then two Blue Note albums of his own music produced with Bob Belden, Snide Remarks (recorded February 1995) and Telepathy (recorded September 29 and 30, 1996), the second a live-to-two-track session with Seamus Blake, Steve Wilson, Bill Carrothers, and Larry Grenadier. In 1999 he was one of three drummers, with Elvin Jones and Jeff Watts, in Michael Brecker's organ-trio album Time Is of the Essence (Verve), and he toured and recorded with Brecker and with Pat Metheny; his time with Metheny, in a trio with bassist Grenadier, produced Trio 99 to 00 and the live Trio to Live (both Warner Bros., 2000).

From the 2000s Stewart worked in a spread of long partnerships. He joined pianist Kevin Hays and bassist Doug Weiss in a trio that recorded five albums, recorded duets with Bill Carrothers in Minneapolis in June 1999 (Duets with Bill Stewart), and played on albums by Scott Colley, Marc Copland (with Gary Peacock, in the New York Trio Recordings series for Pirouet), Chris Potter (Traveling Mercies, 2002, and the live Lift from the Village Vanguard), Jon Gordon, Jim Rotondi, Lage Lund, Seamus Blake, and Peter Bernstein, whose quartet he joined on Let Loose (2016, Smoke Sessions). He led the Bill Stewart Trio with Goldings and Hays on Keynote Speakers (recorded January 2002, issued 2005), then Incandescence (recorded December 2006, Pirouet, 2008), Space Squid (Pirouet, 2015), and a saxophone-and-bass trio with Walter Smith III and Larry Grenadier on Band Menu (2018). The Goldings/Bernstein/Stewart trio kept recording: Earth Tones (1998), Live at Smalls (2011), Ramshackle Serenade (2014), Toy Tunes (2018), Perpetual Pendulum (2022, Smoke Sessions), and Rhombus (Smoke Sessions, released August 2026).

His Scofield association resumed in the 2000s and has produced much of his recent work: EnRoute (2004), This Meets That (2007), Past Present (2015, with Lovano and Grenadier), Country for Old Men (2016, with Swallow and Goldings), Combo 66 (2018), and two ECM trio albums, Swallow Tales (2020, with Steve Swallow) and Uncle John's Band (2023, with bassist Vicente Archer). Past Present and Country for Old Men each won the Grammy Award for Best Jazz Instrumental Album, at the ceremonies of February 2016 and February 2017. Stewart also appears on Solid Jackson (Criss Cross, 2024), the reunion of the M.T.B. quartet of Brad Mehldau, Mark Turner, and Peter Bernstein with Larry Grenadier, recorded in November 2023, and led a quartet with Walter Smith III and Grenadier on Live at the Village Vanguard (Criss Cross, 2025). Zildjian's K Custom Dry Complex rides were developed with him and first sold in 2004, and the company has made a Bill Stewart Artist Series drumstick.

Stewart is a conversational drummer rather than a groove-keeper: he has said that Scofield dislikes a fixed repeating beat and that he likes to be interactive too, so what he plays on a given tune changes from bar to bar, with enough room in a guitar trio for the drums and bass to answer the soloist. He balances that against stability, and says that in funk settings such as his year with Maceo Parker he leaves the interaction aside and holds the tempo and feel. Unlike most jazz drummers he plays matched grip. He is largely self-taught, says his approach came from some fifty people rather than one teacher, and composes at the piano; Joe Lovano has described his writing as that of a melody player working inside the concept of rhythm. He is best known as the drummer in the long-running Goldings/Bernstein/Stewart organ trio and in John Scofield's quartets and trios, and his own albums, mostly of his originals for small groups with saxophone and piano or organ, are the other half of the picture.