He joined the Royal Navy in 1802, was commissioned in 1808, and served in the Napoleonic wars, notably as a lieutenant in Captain Samuel Pym's disastrous attack on Mauritius in August 1810.
After the destruction of his ship, the Magicienne, Wauchope set off in a cutter to Réunion, 140 miles away, to warn Commodore Josias Rowley.
He became "born again of the Holy Spirit"[2] in 1819 and expressed his disapproval to Admiral Robert Plampin of his "living openly with a kept mistress".
In 1818 Wauchope became interested in developing a method of signalling from an observatory to ships the exact time so that the chronometers on board could be rated.
He was allowed to take command of HMS Thalia in June 1834 and was again stationed at the Cape where he became an intimate friend of Sir John Herschel.
In that year he published an anti-Darwinian pamphlet, Proofs of the Possible Cause and Recent Date of the Boulder Drift, Connecting it with the Post Tertiary Period and Noachian Deluge, and wrote his memoirs, A Short Narrative, for the instruction of his great nephew, Andrew Gilbert Wauchope.