[4] On April 25, 1862, the day before New Orleans fell to the US Navy fleet under Admiral David Farragut, the Confederate state government decided to abandon Baton Rouge, moving first to Opelousas, and then to Shreveport.

On May 9, Navy Commander James S. Palmer of the federal gunboat USS Iroquois landed at the town wharf and took possession, without resistance, of the Pentagon Barracks and the arsenal.

On May 29, US Brigadier General Thomas Williams arrived with six regiments of infantry, two artillery batteries, and a troop of cavalry, and began the occupation of Baton Rouge.

During the summer, Major General Earl Van Dorn, commander of Confederate forces east of the Mississippi, resisted a Union bombardment of Vicksburg.

The Confederate ironclad ram Arkansas had come down the Yazoo River, inflicting damage on the unprepared Union fleet as she passed through, and was anchored in Vicksburg.

Breckinridge moved to the Comite River, 10 miles (16 km) east of Baton Rouge, by August 4, and then marched the men closer at night.

Her commander ordered Arkansas set afire to prevent her capture.Without any prospect of naval support, Breckenridge was unable to attack the Union positions and withdrew.

The "Battle of Baton Rouge Commemorative Ceremony" is held every year on the first Saturday in August in and around Magnolia Cemetery, sponsored by the Foundation for Historical Louisiana.