The British band The Rolling Stones named themselves after Muddy Waters' 1950 song "Rollin' Stone". Jimi Hendrix recalled that "I first heard him as a little boy and it scared me to death". The band Cream covered "Rollin' and Tumblin'" on their 1966 debut album, Fresh Cream. Eric Clapton was a big fan of Muddy Waters while growing up, and his music influenced Clapton's music career. "Rollin' and Tumblin'" was also covered by Canned Heat at the Monterey Pop Festival and later adapted by Bob Dylan on his album Modern Times. One of Led Zeppelin's biggest hits, "Whole Lotta Love", has its lyrics heavily influenced by the Muddy Waters hit "You Need Love" (written by Willie Dixon). "Hoochie Coochie Man", was covered by Allman Brothers Band, Humble Pie, Steppenwolf, Supertramp and Fear. In 1993, Paul Rodgers released the album Muddy Water Blues: A Tribute to Muddy Waters, on which he covered a number of his songs, including "Louisiana Blues", "Rollin' Stone", "(I'm your) Hoochie Coochie Man" and "I'm Ready" in collaboration with guitarists such as Gary Moore, Brian May and Jeff Beck. Angus Young, of the rock group AC/DC, has cited Muddy as one of his influences. The AC/DC song title "You Shook Me All Night Long" came from lyrics of the Muddy Waters song "You Shook Me", written by Willie Dixon and J. B. Lenoir. Earl Hooker first recorded it as an instrumental, which was then overdubbed with vocals by Muddy Waters in 1962. Led Zeppelin also covered it on their debut album.[citation needed.

In 1981 ZZ Top guitarist Billy Gibbons went to visit the Delta Blues Museum in Clarksdale with The Blues magazine founder Jim O'Neal. The museum's director, Sid Graves, brought Gibbons to visit Waters original house, and encouraged him to pick up a piece of scrap lumber that was originally part of the roof. Gibbons eventually converted the wood into a guitar. Named Muddywood, the instrument is now exhibited at the Delta Blues Museum in Clarksdale.

Following his death, fellow blues musician B.B. King told Guitar World magazine, "It's going to be years and years before most people realize how greatly he contributed to American music." John P. Hammond told Guitar World magazine, "Muddy was a master of just the right notes. It was profound guitar playing, deep and simple ... more country blues transposed to the electric guitar, the kind of playing that enhanced the lyrics, gave profundity to the words themselves."[67]

Muddy Waters' songs have been featured in long-time fan Martin Scorsese's movies, including The Color of Money, Goodfellas, and Casino. A 1970s recording of his mid-'50s hit "Mannish Boy" was used in the films Goodfellas, Better Off Dead, Risky Business, and the rockumentary The Last Waltz. In 1988 "Mannish Boy" was also used in a Levi's 501 commercial and re-released in Europe as a single with "(I'm your) Hoochie Coochie Man" on the flip side.

The absolute most famous/important guitar riff in the history of the blues. Maybe even the history of music. This one riff inspired a whole helluva lot of people.