Assigned to the 90-gun HMS "Namur", Clephan served as her Second Lieutenant until the Peace of Amiens in April 1802. Taking the opportunity to marry during this brief interval, in March 1803 Clephan was appointed First Lieutenant of the 74-gun HMS "Spartiate", which had been captured from the French during the Battle of the Nile. He was on board "Spartiate" during the Battle of Trafalgar in 1805, after which he was presented with the ship's Union Jack as a mark of esteem from the crew. He served on board "Spartiate" until December 1809.