Bonar studied at Edinburgh; was minister at Collace, Perthshire, 1838 – 1856 (both in the Church of Scotland and the Free Church); and of Finnieston Free Church, Glasgow, 1856 till his death. He joined the Free Church in 1843, and was its moderator in 1878. He was identified with evangelical and revival movements and adhered to the doctrine of premillennialism. With Robert Murray McCheyne he visited Palestine in 1839 to inquire into the condition of the Jews there. During the visit of Dwight L. Moody to Britain in 1874 and 1875, Moody was warmly welcomed by Bonar, despite the latter receiving considerable criticism from other Calvinist ministers in the Free Church.
Bonar also edited Samuel Rutherford's Letters (1863); Letters of Samuel Rutherford, Religious Tract Society, London 1891 and wrote many tracts, pamphlets, and minor biographies.
His daughter Marjory edited his Diary and Letters, his Reminiscences, Heavenly Springs (ISBN 0-85151-479-0) (Portions selected from his diary, letters, and sermons), and Wayside Wells (Thoughts for Sabbath evenings, selected from his writings and sermons).
in-print publications include containing the Diary and Letters and the Reminiscences is: