Nathaniel Magruder was the son of John Magruder and Susanna Smith. He was one of four men elected by the Convention of Maryland on July 3, 1776, to be judges of the new convention for the express purpose of forming a new government. In 1779-1780 he was a Captain in the Maryland Line. He rendered patriotic service by providing wheat for the military on August 8, 1780.
Nathaniel married Margaret Magruder, daughter of James Beall Magruder and Barbara Coombs. They resided at Dunblane, on family land that Nathaniel inherited from his father. A memorial stone was placed in the family cemetery on 11 October 1915 by the members of the Magruder Chapter of the DAR.