Bertram Boltwood was born on July 27, 1870, in the Amherst, Massachusetts home of his grandfather, Lucius Boltwood. After relocating from England in the 17th century, the Boltwood family was active in the Amherst community for generations. Lucius was the son of a farmer who worked his way through Williams College to become a lawyer. He was a founder of Amherst College and ran for Governor of Massachusetts as an early member of the Liberty Party in 1841. Thomas Kast Boltwood, son of Lucius, was a lawyer who died in 1872 when his son Bertram was 2 years old. Bertram Boltwood was emotionally close with his mother, Margaret Mathilda, and he grew up in her hometown of Castleton, NY. She prepared him to attend Yale, his father's alma mater, by placing him in private school at a young age, followed by the Albany Academy.
Boltwood’s childhood reveals influences and inclinations that foreshadow the scientist he became as an adult. As a boy, he was interested in mechanical gadgets and enjoyed hobbies such as fishing, photography, and minerals. The latter was likely the influence of his uncle, Charles Upham Shepard, who was a mineralogist and a chemist. His personality was reportedly light-hearted, and he was known to play practical jokes in his youth. He was often reminded of a familial tie to Ralph Waldo Emerson through his paternal great grandmother’s sister (Emerson’s mother Ruth Haskins), and it was expected that Boltwood would study and succeed in line with the family legacy.