Johnston was born in 1872 in Evansville, Ind. She was the stepdaughter of Annie Fellows Johnston, also of Evansville, who wrote the "Little Colonel" books and moved to Pewee Valley, Ky., after visiting in the 1890s. The Johnstons lived at The Beeches. Patty Thum's celebrated and nationally reproduced painting "The Lady of the Lilies," in the Speed Art Museum collection, is a portrait of Mary Johnston in her garden at The Beeches. She dearly loved her garden, as one family historian put it. Johnston studied with Richard Miller and in Cincinnati with G. E. Hopkins. She was active in local exhibitions from 1927 to 1939. She lived at The Beeches until her death in the 1940s.