Webster was married twice — first in 1808 to Grace, daughter of Rev. Elijah Fletcher, a New Hampshire clergyman. She died in 1828, leaving two sons, (Daniel) Fletcher, killed in the Civil War, and Edward, a major in the United States army, who died while serving in the Mexican–American War, and a daughter Julia, who married Samuel Appleton. A daughter, Grace, and a son, Charles, died young. Webster's second wife was Caroline LeRoy, daughter of Herman Le Roy, a New York merchant. He was married to her in December 1829 and she survived him, dying in 1882.