He was the son of Lewis Bogardus (1738–1808) and Annie (Mills) Bogardus (b. 1745). In 1792, he married Maria Sabina Waldron (1774–1855), and they had ten children.
He fought in the War of 1812, and in November 1812, as a lieutenant colonel, was placed in command of the Third Brigade of the New York Militia Infantry. From 1813 to 1815, as a colonel, he commanded the 41st U.S.Infantry Regiment. He was later promoted to general.