In 1871, Hughes-Hallett married Catherine Rosalie Greene, the widow of Sir Charles Jasper Selwyn and of Reverend Harry Dupuis.
In 1882, Hughes-Hallett wed a middle-aged American heiress, Emilie Page von Schaumberg (1833-1923), the daughter of James von Schaumberg and Caroline Page, but the marriage ran into difficulties five years later, when Hughes-Hallet was caught in liaison with his first wife's stepdaughter, Beatrice.