Promoted to commander on 20 October 1831, Codrington became commanding officer of the sloopHMS Orestes in the Mediterranean Fleet in June 1834.[4] Promoted to captain on 20 January 1836, he became commanding officer of the sixth-rateHMS Talbot in March 1838 and in that capacity undertook a survey of enemy positions prior to the bombardment of Acre in November 1840 during the Egyptian–Ottoman War.[4] For this service he was appointed a Companion of the Order of the Bath.[2]
Codrington went on to command the first-rate HMS Queen, his father's flagship as Commander-in-Chief, Portsmouth, in March 1841 and then to command the first-rate HMS St Vincent, his father's next flagship as Commander-in-Chief, Portsmouth, in October 1841.[4] He became commanding officer of the fifth-rate HMS Thetis in the Mediterranean Fleet in October 1846 and provided refuge on board ship for Leopold II, Grand Duke of Tuscany and his family who were fleeing from revolutionary forces in 1848.[4]
Codrington became commanding officer of the first-rate HMS Royal George in the Baltic Sea in October 1853 and took part in naval operations during the Crimean War.[4] Admiral Sir Charles Napier threatened to court-martial him for failing to achieve the required standards but the Admiralty refused to support this course of action.[4] Promoted to commodore, he was given command of a squadron of gunboats with his broad pennant in the second-rate HMS Algiers in February 1856.[4] The Admiralty envisaged that he would lead a mission to attack the naval base at Kronstadt but the War ended with the Treaty of Paris in March 1856 and the mission was abandoned.[4]
In April 1849 Codrington married Helen Jane Webb (1828–1876); they had two daughters.[4] They had a much publicised divorce in 1864 in which the Admiral accused her of having a close relationship with the women's rights activist Emily Faithfull.[11] This notorious legal case, the Codrington Affair, was fictionalisd by Emma Donoghue in The Sealed Letter (2008).[12] The novel was joint winner of the 2009 Lambda Literary Award for Lesbian Fiction.[13]
He married Catherine Aitchison (née Compton) in August 1869; they had one daughter.[6]
Ellen Codrington, the younger of the two daughters from Henry Codrington's first marriage, married in 1878 John Roche Dasent, the eldest son of George Webbe Dasent, the translator of Norse mythology.[14]