During the Civil War, Natchez remained largely undisturbed, but not entirely. Natchez surrendered to Flag-Officer David G. Farragut after the fall of New Orleans in May 1862.[3] In September, 1863, the Union ironclad USS Essex,[4] under Capt. William D. Porter shelled the town but caused only minor damage, although a seven year-old Jewish girl named Rosalie Beekman was tragically killed.[5][6] Union troops under Ulysses S. Grant occupied Natchez in 1863; Grant set up his temporary headquarters in the Natchez mansion Rosalie.[7] Confederate army forces attempted to recapture Natchez in December 1863 but did not attack the town itself because the C.S.A. forces were outnumbered.[8]

Like almost everywhere else in the United States, numerous Natchez residents did in fact fight or otherwise participate in the war and many families lost their antebellum fortunes. The fact that the town was largely spared the horrors of the war is illustrated by the legend of the Battle of Natchez. According to this story, while Union troops were being housed in Natchez, civilians and regular bar owners gathered at the river landing to watch Union gunboats travel the Mississippi River from Vicksburg down to New Orleans. In one passing, a Union gunboat fired a blank from a canon to rile up the Union troops at Fort Rosalie. This caused an elderly man to have a heart attack at Under the Hill–the one casualty in the Battle of Natchez.[9]

Despite the city's relatively peaceful atmosphere under Union occupation, Natchez residents remained somewhat defiant of the Federal authorities. In 1864, the Roman Catholic bishop of the Diocese of Natchez, William Henry Elder, refused to obey a Federal order to compel his parishioners to pray for the President of the United States. In response, the Federals arrested Elder, jailed him briefly and then banished him across the river to Confederate held Vidalia, Louisiana. Eventually Elder was allowed to come back to Natchez and resumed his clerical duties there until 1880, when he was elevated to archbishop of Cincinnati.