He died in 1873 and is buried with his wife Mary Thom (1813-1858) in a crowded section of Dean Cemetery east of the new Dean Gallery entrance and north-east of the distinctive pyramid therein with a strange back-to-back monument with his son Thomas (1838-1896), designed by David Watson Stevenson. His sons, William Dundas Bonnar, engraver (1831-1855) and Thomas Bonnar (d. 1899) are buried with them.