The son of James Bonar, Solicitor of Exise for Scotland, he was born and educated in Edinburgh. He comes from a long line of ministers who have served a total of 364 years in the Church of Scotland. One of eleven children, his brothers John James and Andrew Alexander were also ministers of the Free Church of Scotland. He had married Jane Catherine Lundie in 1843 and five of their young children died in succession. Towards the end of their lives, one of their surviving daughters was left a widow with five small children and she returned to live with her parents. Bonar's wife, Jane, died in 1884. He is buried in the Canongate kirkyard.