Ebenezer Emmons was born in Middlefield, Massachusetts. He attended Williams College in Williamstown, Massachusetts, studied medicine in Albany, New York, and geology at the Rensselaer School in New York, under Amos Eaton. He taught the natural sciences at Williams College and chemistry and obstetrics at Albany Medical College.
Emmons's main interest was geology. He is known for naming New York's Adirondack Mountains and being the first to ascend Mount Marcy in that mountain range. He was Chief State Geologist on the geological survey of northern New York, on which Edward Hitchcock also briefly worked. During the survey, Emmons recognized that overlying rock layers in what he named the Taconic System, east of the Hudson River, were older than the rocks beneath them. He and his former student James Hall disagreed vehemently over this. Time proved Emmons correct, but he did not win in the short run. A court decision went in Hall's favor and Emmons had to leave New York. He moved to North Carolina and became the first State Geologist there, a position he held until his death.