John S. Clark was born on November 2, 1823, in Mentz, New York.

His original name was John Swarthout Smith Duvall, and it was changed to John Clark “by an act of the legislature” according to the wish of his grandfather Benoni Clark, who made him his heir. He attended Bethany College in West Virginia and later became a civil engineer and surveyor in Cayuga County. In May of 1861, he was selected as Colonel in command of the newly forming 19th Regiment of New York Volunteers who left for Washington and the Union Army. Clark's main task was as a military topographer. When he returned to civilian life, he became the City Engineer and Surveyor of Auburn, New York. He also allowed his interests in history and archaeological topography to flourish. He was in communication with many of the eminent 19th-century archeologists and historians of the Northeastern United States. He tried to locate formerly occupied native villages in upstate New York and wrote about the Native American archeology along the Susquehanna River. He also wrote “General Sullivan's Campaign against the Western Indians” (1879), as well as the so-called “Groveland Massacre". He received a Cornplanter medal given for excellence in Iroquois Research.

In 1842, he married Mary Ann Crofoot (1821–1887). In 1887, he remarried Euretta Eggleston Welsh (1845–1923). He died on April 7, 1912, in Auburn, Cayuga County, New York.