In 1827 Fowler was appointed Professor of Chemistry and Natural History at Middlebury, and served in that position until 1838. He left Middlebury to accept the position of Professor of Rhetoric and Oratory at Amherst College, 1838-1843. Fowler lived in Amherst, Massachusetts, until 1856. He later served as a member of the Massachusetts Assembly and the Connecticut Senate.
For his father-in-law Noah Webster, Fowler edited the university edition of Webster’s Dictionary. His works include English Grammar; The English Language in its Elements and Forms; Memorials of the Chaunceys; The Sectional Controversy, or Passages in the Political History of the United States; William Fowler, the Magistrate, and his Descendants; Wives of the Fowlers; Wives of the Chaunceys; History of Durham; Local Law in Massachusetts and Connecticut; Conditions of Success in Genealogical Investigation.
On July 21, 1825, Fowler married Elizabeth (Webster) Cobb, with whom he had four children.
William Fowler died in Durham, Connecticut, on January 15, 1881.