After 1660
Denham became a Member of Parliament for Old Sarum in 1661, became a Fellow of the Royal Society on 20 May 1663, and became a Knight of the Bath.
After the Restoration Denham became Surveyor of the King's Works, probably for reasons of his earlier political services rather than for any aptitude as an architect. John Webb, who, as Inigo Jones's deputy had the competence to have served in the post, and complained "though Mr. Denham may, as most gentry, have some knowledge of the theory of architecture, he can have none of the practice and must employ another." There is no evidence that he personally designed any buildings, although he seems to have been a competent administrator. John Webb was appointed Denham's deputy by 1664 and did Denham's work at Greenwich (from 1666) and elsewhere.
Denham made an unhappy marriage, and his last years were clouded by dementia. With Denham's increasing mental incapacity, Charles II requested in March 1669 that Christopher Wren be appointed Denham's "sole deputy"; Wren succeeded him as King's Surveyor upon his death two weeks later. Denham was buried in Poets' Corner of Westminster Abbey.
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