In command of the West Gulf Blockading Squadron, with his flag in USS Hartford, in April 1862 he ran past Fort Jackson and Fort St. Philip and the Chalmette, Louisiana, batteries to take the city and port of New Orleans, Louisiana, on April 29 that year, a decisive event in the war. His country honored its great sailor after New Orleans by creating for him the rank of rear admiral on July 16, 1862, a rank never before used in the U.S. Navy. (Before this time, the American Navy had resisted the rank of admiral, preferring the term "flag officer", to separate it from the traditions of the European navies.) Later that year he passed the batteries defending Vicksburg, Mississippi. Farragut had no real success at Vicksburg, where one makeshift Confederate ironclad forced his flotilla of 38 ships to withdraw in July 1862.

He was a very aggressive commander but not always cooperative. At the Siege of Port Hudson the plan was Farragut’s flotilla would pass by the guns of the Confederate stronghold with the help of a diversionary land attack by the Union Army of the Gulf, commanded by General Nathaniel Banks, to commence at 8:00 am March 15, 1863. Farragut unilaterally decided to move the time table up to 9:00 pm, March 14th and initiate his run past the guns before Union ground forces were in position. By so doing the uncoordinated attack allowed the Confederates to concentrate on Farragut’s flotilla and inflict heavy damage on his warships.

Farragut’s battle group was forced to retreat with only two ships able to pass the heavy cannon of the Confederate bastion. After surviving the gauntlet Farragut played no further part in the battle for Port Hudson and General Banks was left to continue the siege without advantage of naval support. The Union Army made two major attacks on the fort and both were repulsed with heavy losses. Farragut’s flotilla was splintered yet was able to blockade the mouth of the Red River with the two remaining warships, but not efficiently patrol the section of the Mississippi between Port Hudson and Vicksburg. Farragut’s decision thus proved costly to the Union Navy and the Union Army which suffered the highest casualty rate of the Civil War at the Battle of Port Hudson.

Vicksburg surrendered on July 4, 1863, leaving Port Hudson as the last remaining Confederate stronghold on the Mississippi River. General Banks accepted the surrender of the Confederate garrison at Port Hudson on July 9, 1863 ending the longest siege in US military history. Control of the Mississippi River was the centerpiece of Union strategy to win the war and with the surrender of Port Hudson the Confederacy was now severed in two.

On August 5, 1864, Farragut won a great victory in the Battle of Mobile Bay. Mobile, Alabama, at the time was the Confederacy's last major port open on the Gulf of Mexico. The bay was heavily mined (tethered naval mines were known as torpedoes at the time). Farragut ordered his fleet to charge the bay. When the monitor USS Tecumseh struck a mine and sank the others began to pull back.

Farragut could see the ships pulling back from his high perch, lashed to the rigging of his flagship the USS Hartford. "What's the trouble?" was shouted through a trumpet from the flagship to the USS Brooklyn. "Torpedoes!" was shouted back in reply. "Damn the torpedoes!" said Farragut, "Four bells. Captain Drayton, go ahead! Jouett, full speed!" The bulk of the fleet succeeded in entering the bay. Farragut then triumphed over the opposition of heavy batteries in Fort Morgan and Fort Gaines to defeat the squadron of Admiral Franklin Buchanan.

He was promoted to vice admiral on December 21, 1864, and to full admiral on July 25, 1866, after the war.

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