[2][3][4] Cooper's next assignment was to the frigate USS Macedonian, the flagship of the Africa Squadron, engaged in the African Slave Trade Patrol, serving aboard her as an acting master.

He later transferred to the sloop-of-war USS Saratoga, also in the Africa Squadron, and returned to the United States aboard her in December 1844.

After the American capture of Mexico City in September 1847, Flirt detached from Conner's squadron and returned to the United States.

His Susquehanna tour finally came to a close when the ship concluded her cruise at Philadelphia, Pennsylvania, in March 1855 after a voyage from China via the Indian Ocean and Cape of Good Hope.

In November 1862, at the request of the American industrialist and philanthropist Cornelius Vanderbilt, he took command of the steamer USS Connecticut in the West Indies Squadron to escort Vanderbilt's mail steamers on their voyages between Aspinwall, Panama – then a part of the United States of Colombia – and New York City.

He became commanding officer of the sidewheel gunboat USS Sonoma in 1863 for operations in the South Atlantic Blockading Squadron.

In 1864 he took command of the monitor USS Sangamon and became heavily involved in the blockade of Charleston, South Carolina, operating for seven weeks inside Charleston Roads on picket duty and in support of Union Army forces, and engaging in almost constant shelling of Confederate forces at Fort Sumter and on Sullivan's Island.

[4][5][6] Cooper was ordered to command of the North Atlantic Squadron in 1882, at one point attending the unveiling of a statue of George Washington at Caracas, Venezuela.

One son, also named George H. Cooper, drank excessively and was chronically unemployed, subsisting on a generous amount of money his parents sent him, and was arrested in September 1885 for theft from a boarding house where he was staying in Brooklyn, New York.

[10] Another son, Mason S. Cooper, born in 1847 in Portsmouth, Virginia, served in the U.S. Navy during the American Civil War, reaching the rank of ensign, spent 14 years as a captain of merchant ships of the Pacific Mail Steamship Company, was an inspector in the New York Custom House, and later became an admiral in command of the Haitian Navy; he died suddenly on 2 January 1891 in Brooklyn.