His daughter Natalie Scarritt Wales (1909-2013), best known as Lady Natalie Malcolm Douglas-Hamilton, was a socialite and philanthropist known for organizing the "Bundles for Britain" campaign during World War II. His son Nathaniel Brackett Wales, Jr. (1915–1969) graduated from Harvard College in 1937. He was a physicist and inventor with over 75 patents.
In 1908 in Bridgewater, Massachusetts, Nathaniel B. Wales, Sr. married Enid Mariner Scarritt (1889-1972).[2] They had two children and were divorced in July 1923. In 1928, he married Mary van Wagenen Terry. His final wife was Madge Mariner (1885-1978).