In 1886, Herbert Putnam married Charlotte Elizabeth Munroe of Cambridge, Massachusetts, and together they had two daughters, Shirley and Brenda Putnam. Brenda Putnam grew up to become a celebrated sculptor in the early 20th century, highly known for her "children, cherubs, and garden ornaments." Throughout Herbert Putnam's career, he was described by his colleagues as maintaining "an impenetrable dignity…formal manner, invariable gracious and cordial, covered shyness and a deep reserve. He had few intimates, even among his closest colleagues, but he was fond of good company and good conversation" as well being "painfully modest, a family man who had an unreciprocated view of his staff as family."