After the Rebellion, he bought an estate in County Wicklow, and in 1802, married, at Dublin, Alicia Weldon, who is variously described as being the daughter of Lady Weldon, and a niece of the Earl of Dysart, though which ones are meant is not specified. C.H. Mackintosh's mother was Leonora Sophia (d. 1891), daughter of Col. Dickinson, of Jamaica, British West Indies. Through the maternal line, Mackintosh claimed to be close kin to Sir Stamford Raffles, founder of Singapore, one of whose sisters was called Leonora, and one of whose half-aunts, Elizabeth Raffles, married William Carter, Esq., of Jamaica. Paternally, he claimed to be a near relation of the essayist and politician, the Right Honourable Sir James Mackintosh, who was member of the Kellachie branch of the Inverness-shire-based Clan Mackintosh, part of the Scottish Highlands Chattan Confederation.