In the spring of 1903, Carter met Gertrude Codman Parker (born 6 February 1875). She was travelling in the Bahamas with her parents. Carter and Parker got married on 25 August 1903 in the Church of the Advent in Boston, USA. He had been married before this, and had three sons and two daughters. His son Humphrey was Director of the Cambridge University Botanic Garden. He had one son from his second marriage, named John Carter, who was a Senior Engineer for Westinghouse Electric. 