The second and third floors of the museum are entirely dedicated to exhibitions. Special temporary exhibitions focusing on individual artists or on the work of women from a particular state, country, or region are held on the second floor. Establishing the Legacy, on the third floor, is a selection of works from the permanent collection, that provides visitors with a continuous record of women's achievements in the visual arts from the sixteenth century through the twentieth century.

On the fourth floor is NMWA's Library and Research Center, which houses extensive collections of materials on women artists and has an ongoing exhibition program of book-related arts. The Eulabee Dix Gallery, which is also located on the fourth floor, alternates special exhibitions and work by Dix. The fifth floor houses the museum performance hall, where many public programs are held. Staff offices occupy the fourth, fifth, and sixth floors; the museum receptionist is on the fourth floor.