His father was the biologist Thomas Henry Huxley.
He married firstly Julia Arnold, a sister of the novelist Mrs. Humphrey Ward, niece of the poet Matthew Arnold, and granddaughter of Dr. Thomas Arnold, the headmaster of Rugby School who was immortalised as a character in the novel Tom Brown's Schooldays. Their children were/included the biologist Sir Julian Sorell Huxley and the writer Aldous Leonard Huxley.
After the death of his first wife, Leonard married Rosalind Bruce (said to be related in some way to Robert the Bruce), and had two further sons. The younger of these was the physiologist Andrew Fielding Huxley.