Thomas B. Waterman succeeded his father, Capt. Thomas Waterman, in the shipbuilding partnership with Capt. Elijah Barstow. 

Thomas B. only had one sibling, a sister, Sylvia, who died in August, 1844. 

He married Clara Crooker of Norwell, and they had two children: Thomas W., born May 4, 1868, and taken from them by typhoid fever in the fall of 1888, and George, born October 30, 1870, who later worked in a bank in Boston.