Muldaur began her career in the early 1960s as Maria D'Amato, performing with John Sebastian, David Grisman, and Stefan Grossmanas a member of the Even Dozen Jug Band. During this time, she was part of the Greenwich Village scene that included Bob Dylan, and some of her recollections of the period, particularly with respect to Dylan, appear in Martin Scorsese's 2005 documentary film No Direction Home.
She married fellow Jug Band member Geoff Muldaur, and after the Kweskin outfit broke up, the two of them produced two albums. She began her solo career when their marriage ended in 1972, but retained her married name.
Her first solo album, Maria Muldaur, released in 1973, contained her hit single "Midnight at the Oasis", which reached number 6 on the BillboardHot 100 in 1974. It also peaked at number 21 in the UK Singles Chart.Later that year, she released her second album, Waitress in a Donut Shop. This included a re-recording of "I'm a Woman", the Leiber and Stoller number first associated with Peggy Lee and a standout feature from her Jug Band days. The title of this album is taken from a line in another song on the album, "Sweetheart", by Ken Burgan.
Around this time, Muldaur established a relationship with the Grateful Dead. Opening for some Grateful Dead shows in the summer of 1974, with John Kahn, bassist of the Jerry Garcia Band, eventually earned her a seat in that group as a backing vocalist in the late 1970s. Around the same time Muldaur met and eventually collaborated with bluegrassicon Peter Rowan.
Her 2005 release Sweet Lovin' Ol' Soul was nominated for both a Blues Music Award (formerly the W.C. Handy Award) and a Grammy Award in the Traditional Blues category. In 2013, she was nominated for a Blues Music Award in the Koko Taylor Award (Traditional Blues Female) category.