Hotham was given command of the 64-gun on 14 March 1803 and assigned to serve in the North Sea and the English Channel. He was employed in the blockade of the invasion flotilla at Boulogne, but his health declined while on this service, and he resigned the command on 8 September 1803. He came ashore, and on 12 June 1804 married Anne Jeynes, sister-in-law of Admiral Sir Edward Thornbrough. On 25 May 1808 he returned to semi-active service commanding the Sea Fencibles at Liverpool. He held this position until 28 February 1810. On 31 August 1812 he became commander of the yacht , received a promotion to rear-admiral on 4 December 1813, and relinquished command of her on 2 April 1814. He was offered the command of one or two dockyards, but declined them in the hope of being offered a command afloat. Nothing could be found for him however. He became a gentleman-in-waiting at court, later writing a manuscript book entitled "Characters, Principally Professional", and was one of the first appointments as Knight Commander of the Order of the Bath on the restructuring of the order on 2 January 1815. He was advanced to vice-admiral on 19 July 1821, and to full admiral on 10 January 1837. He became a Knight Grand Cross of the Order of the Bath on 4 July 1840. Sir William Hotham died at New Windsor, Berkshire on 31 May 1848 at the age of 76. He was buried on 7 June in the family vault at Binfield, Berkshire.