Waggaman was born on September 21, 1846 to John and Ester (Cottrell) McKee. She was from Baltimore and attended Mount de Sales Academy in Catonsville, Maryland. Her mother died when she was young, and she moved with her father to New York during the American Civil War. Her father was arrested because of his support for the American South, and Waggaman would write "An American Bastile" about her experiences during the Civil War that was published in Ave Maria. After the Civil War she returned to Mount de Sales Academy and was valedictorian of her class in 1864.
