On March 6, 1745, Wooster married Marie Clapp, the daughter of Yale's president, Thomas Clapp. They went on to have four children; their son Thomas also served in the American Revolutionary War. His grandson Charles Whiting Wooster was Commander-in-Chief of the Chilean Navy. Shortly after his marriage, David Wooster was named captain of a company in the provincial regiment of Andrew Burr (uncle to future United States Vice President Aaron Burr), and saw service at that year's Siege of Louisbourg. He was sent to France as part of the prisoner escort following that action, and then to England, where he was given an audience with King George and a position as captain in the regiment of William Pepperrell in the British Army.