Mark Ellis was born on 16 August 1960 in London, England. As a child, Ellis attended St Olave's Grammar School in Orpington, England. He began his music career as the vocalist for the band Seven Hertz. During that same time, he began his professional studio career as a runner at Morgan Studios in London, where he also served as Tape Operator on 1984 by Rick Wakeman. Ellis also was a runner at Battery Studios in London and held apprenticeships at Marcus Studios and Trident Studios.
Flood moved up to house engineer before going freelance in 1981, the same year he worked as assistant engineer on New Order's debut album, Movement. The following year, he engineered Ministry's debut album, With Sympathy. He then became associated with Stevo's Some Bizzare Records label, leading to work with Cabaret Voltaire, Psychic TV, and Marc Almond's side project, Marc and the Mambas, among others.
Following his work with Some Bizzare Records, Flood began working with Mute Records as their preferred producer, heralding his first production project with Nick Cave and the Bad Seeds on From Her to Eternity (19831984) and the follow-up album, The Firstborn Is Dead (1984). His work at Mute was as producer, co-producer or engineer with each of the label's major acts, including Depeche Mode, Vince Clarke and Erasure, whose debut album Wonderland (1986) and its followup The Circus (1987) he engineered.
Flood's first mainstream commercial break came in 1987 when he engineered U2's The Joshua Tree alongside producers Brian Eno and Daniel Lanois. Shortly thereafter he co-produced Nine Inch Nails on debut Pretty Hate Machine along with John Fryer, Adrian Sherwood, and Keith LeBlanc. He also worked with Depeche Mode on their 1990 album, Violator. In 1991 he returned to work again with U2 on Achtung Baby along with Brian Eno, Daniel Lanois and Steve Lillywhite. The following year, he also returned to work with Depeche Mode to record the album Songs of Faith and Devotion and co-produced three tracks of Nine Inch Nails' Broken EP.
In 1993, Flood shifted from engineering U2's albums to producing them, sharing duties with Brian Eno on Zooropa. In 1994, he worked again with Nine Inch Nails, this time on The Downward Spiral. In 1995 Flood co-produced The Smashing Pumpkins' album Mellon Collie and the Infinite Sadness with longtime collaborator Alan Moulder, and PJ Harvey's album To Bring You My Love. Shortly thereafter, he assisted producer Nellee Hooper on Sneaker Pimps' Becoming X. He also collaborated with Dave Bessell, Gary Stout and Ed Buller to create Node; an analogue synth heavy project that produced a single album, Node.
In 1996 Flood teamed up with U2 once again to produce Pop, released the next year. The following year, he assisted Billy Corgan and Brad Wood on The Smashing Pumpkins's 1998 album Adore and co-produced PJ Harvey's album Is This Desire?.