Waters was born in Iowa and started singing semi-professionally in high school. After school, she sang for the Jerry Gray Hotel Jazz Band. Her family moved to Denver and she started listening to Billie Holiday, whose life and singing had a profound influence on her.
In the early 1960s she followed the recommendation of friends to move to New York. Albert Ayler heard her in a dining club and introduced her to Bernard Stollman, the owner of the experimental jazz label ESP-Disk. Her most influential albums, Sings (1965) and College Tour (1966) were made for this label.
In the late 1960s, she spent time in Europe and then left the music world to raise her son (born in 1969) in California. Almost 30 years later she recorded the album Love Songs in 1996 and began performing in public again. This included reunion concerts with pianist Burton Greene at two music festivals in May 2003: Visions Festival in New York and Le Weekend in Stirling.
In 2004 she released You Thrill Me: A Musical Odyssey, a collection of rare and unissued recordings from the years 1962–1979. ESP-Disk reissued Sings and College Tour on a single CD (The Complete ESP-Disk Recordings) in 2006.
- Sings (ESP-Disk, 1965)
- College Tour (ESP-Disk, 1966)
- Love Songs (Jazz Focus, 1996)
- You Thrill Me: A Musical Odyssey 1962–1979 (Water, 2004)
- Happiness Is a Thing Called Joe: Live in San Francisco 2002 (DBK Works, 2005)
- The Complete ESP-Disk Recordings (ESP-Disk, 2006)
- What Is the Color When Black is Burned? A Patty Waters Appreciation at Perfect Sound Forever