Command of the ship passed to Captain William Fitzwilliam Owen, who had risen to prominence following his surveys of the Great Lakes. In August 1821, in the company of the brig-sloop Barracouta, Leven departed for Africa again, with orders to map eastward from the Cape of Good Hope. Amending orders later extended the mission to include a survey of the entire east coast of Africa as well as southern Arabia, Madagascar, and several island groups in the Indian Ocean. On their return journey, long stretches of the west African coastline and the River Gambia were surveyed, several slave ships were apprehended and support was given to British forces in the First Anglo-Ashanti War. By the time she returned home late in 1826, 30,000 nautical miles (56,000 km) of coast had been surveyed and 83 charts prepared. This had been achieved at a terrible cost; half the crew of the two little ships had been killed by tropical diseases.
Owen mapped the entire east African coast from the Cape to the Horn of Africa between 1821 and 1826 in the sloop Leven and in company with the brig Barracouta. During this period, Owen established a one man protectorate of Mombasa with the aim of disrupting the ‘hellish trade’ in slaves; but Owen was forced to shut down under orders from the Crown after only three years. When he returned in 1826, with 300 new charts, covering some 30,000 miles of coastline, over half of his original crew had been killed by tropical diseases.
The settlement at Port Clarence (named after the Duke of Clarence) was constructed under the supervision of William Fitzwilliam Owen. He had previously mapped most of the coasts of Africa and was a zealous anti-slaver. During his three-year command, his forces detained 20 ships and liberated 2,500 slaves.
In the mid-1830s, having little hope of further naval appointment, he removed with his family to New Brunswick. He secured title to Campobello Island, which had been granted to his grandfather and was lord proprietor of the same as well being involved in other investments in New Brunswick. From 1841 he served as a justice of the peace as well as concurrently as judge of the Inferior Court of Common Pleas.
Between 1837 and 1842 he was a very visible member of the New Brunswick House of Assembly for Charlotte County. Following his defeat for reelection, he was appointed in December 1843 to the New Brunswick Legislative Council of which he was an active member through 1851.
In the final action of his naval career, between September 1842 and December 1847, he conducted the definitive survey of the Bay of Fundy for the Admiralty. Indeed some charts of the area are still based upon his surveys