He patrolled the Pacific coasts of Mexico and Central America for two years protecting American interests in that area.

In the autumn, he was assigned to special duty in St. Louis, Missouri, to assist in establishing the Western Flotilla to seize and control the Mississippi and its tributaries for the Union.

On 10 January, Essex and St. Louis engaged three Confederate gunboats and forced them to retreat to the protection of Southern shore batteries.

Though still severely hampered by his injuries, Porter directed the extensive repair and renovation of Essex from his sick bed.

Porter completed the renovation of Essex at St. Louis in July and rejoined the Western Flotilla at Vicksburg, Mississippi, later that month.

At dawn on the 22nd, Porter took Essex out to attack the Confederate ironclad ram CSS Arkansas which had recently left the Yazoo River and taken cover under Vicksburg's shore batteries.

As a result, Essex missed her target and ran aground instead, where for ten minutes she remained under fire from both Arkansas and the shore batteries.

On 5 August, his ship and Sumter assisted Union Army troops in repelling a Confederate land attack on Baton Rouge.

Congress recognized the role played by Porter and his ship in June 1864 when they awarded the Essex crew $25,000 in prize money.

Porter's last real action in the war occurred in September 1862 when Essex conducted a bombardment of Natchez, Mississippi,[1][2] and duelled the shore batteries at Port Hudson, Louisiana.