He graduated from Columbia in 1862,[3] and then studied chemistry with Jean Baptiste André Dumas and Charles Adolphe Wurtz in Paris; with Robert Bunsen, Hermann Kopp, and Gustav Kirchhoff at Heidelberg; with Friedrich Wöhler at Göttingen; and with August Wilhelm von Hofmann in Berlin, and received a D. Phil.

In 1874 he was appointed professor of chemistry in the Woman's Medical College of the New York Infirmary.

The celebration of the centennial of chemistry at Northumberland, Pennsylvania, the home of Joseph Priestley, who discovered oxygen in 1774, was suggested and brought about by Bolton.

[3] Among his investigations, that of the action of organic acids on minerals is perhaps the most important, but most of his work was literary, and his private collection of early chemical books was unsurpassed in the United States.

[1] The Science History Institute hosts the Bolton Society, which is named for H.C. Bolton, to support "printed materials devoted to chemistry and related sciences" and to support its Othmer Library of Chemical History.