During the mid-1960s she became involved in the Civil Rights Movement, traveling to the Southern United States to join the Selma to Montgomery march and to participate in voter registration drives.

This project became the Lesbian Herstory Archives, which opened in 1974 in the pantry of the apartment she shared with her then-partner Deborah Edel, and later with her good friend Mabel Hampton,[7] and moved to a brownstone in Park Slope, Brooklyn in 1992.

[9] Her erotica focusing on butch and femme relationships made her a controversial figure during the feminist sex wars of the 1980s; members of Women Against Pornography called for censorship of her stories.

"[4] Her writings on the subject were highly influential; Lillian Faderman describes her as the "midwife" to a revised view of butch and femme,[10] and her 1992 anthology The Persistent Desire: A Femme-Butch Reader became the standard work in its field.

In 1992, Nestle delivered the first Kessler Lecture for the CUNY Center for Lesbian and Gay Studies titled "I Lift My Eyes to the Hill": the Life of Mabel Hampton as Told by a White Woman.