On June 30, 1773, Johnson married Mary Nicoll "Polly" Watts (1751–1815), a daughter of Hon. John Watts, President of the King's Council, of New York. After he escaped to Canada in May 1776 at the outbreak of the American Revolutionary War, Lady Johnson was detained that year by the Whigs of New York as a hostage for the good conduct of her husband. After she was freed to join Sir John in Canada, the couple lived in Montreal during the winter and spent the summers on their seigneury at Argenteuil, Ottawa on the Ottawa River. The couple also visited in England. Together, Mary and Sir John had ten sons, eight of whom served in the British army and navy, and eight daughters, including: