Codrington became commanding officer of the first-rate in the Baltic Sea in October 1853 and took part in naval operations during the Crimean War. 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. Promoted to commodore, he was given command of a squadron of gunboats with his broad pennant in the second-rate in February 1856. 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.