Later, he took an active role in the Mexican–American War, serving as executive officer of the sloop Cyane during the capture of Monterey, California on July 7, 1846, and in the occupation of both San Diego and Los Angeles.

Captain of the steam sloop Pawnee at the outbreak of the American Civil War, he attempted to relieve Fort Sumter and to burn the Norfolk Navy Yard.

In the ensuing explosion, one man was killed and a large hole was torn into the ironclad but she continued her blockading duties.

In December 1870 Rowan reached the mandatory retirement age of 62 but, like admirals Farragut and Porter before him, he was allowed to remain on active duty.

In 1882 Admiral Rowan was elected as a First Class Companion of the District of Columbia Commander of the Military Order of the Loyal Legion of the United States (MOLLUS).