After the Civil War broke out he was named colonel of an infantry regiment and accompanied the New Orleans expedition in 1862.

[2] On 8 March 1862, the first three regiments of Major General Benjamin F. Butler's expedition landed at Ship Island.

[4] Butler's occupation force numbered about 6,000 troops and was made up of six infantry regiments, including Gooding's 31st Massachusetts, two cavalry companies, and three artillery batteries.

[2] On 8 November 1862, Butler was replaced in command of the Department of the Gulf by Major General Nathaniel P. Banks, who was to be reinforced by 10,000 troops.

[7] The Confederates entrenched defense lines on the narrow strips of land on each side of Bayou Teche.

Gooding's men were opposed by the 7th Texas Cavalry Regiment and Brigadier General Alfred Mouton's Louisiana brigade.

[9] Starting at 10:00 am on 13 April, Gooding's men cautiously pressed forward until they reached a position to launch an assault.

[13] At the Siege of Port Hudson (22 May – 9 July 1863), Gooding commanded the 3rd Brigade in Paine's 3rd Division of the XIX Corps.

Banks' orders were not explicit and one of his division commanders willfully disobeyed his instructions, so that the attacks were not simultaneous.

Advancing in the open, the soldiers met withering fire from the defenders and immediately went to ground, unable to get forward, and Paine was badly wounded.

[2] During the Red River campaign, Gooding led the 5th Brigade in Brigadier General Albert Lindley Lee's Cavalry Division, XIX Corps.

[20] On 4 April, while Gooding's brigade was on the east bank of the Red River, Major General A. J. Smith ordered him to clear some of St. John Richardson Liddell's Confederates out of Campti.

Gooding's troopers drove the Confederates out of the town, but needed assistance from the 5th Minnesota Infantry to drive them out of the area.

Though the Union troops repulsed the Confederates at the Battle of Pleasant Hill on 9 April, Banks soon abandoned the campaign.

Hearing that Union soldiers planned to burn down the town, a citizen asked Banks if it were true.