In U.S. history, Natchez is recognized particularly for its role in the development of the Old Southwest during the first half of the 19th century. It was the southern terminus of the historic Natchez Trace, with the northern terminus being Nashville, Tennessee. After unloading their cargoes in Natchez or New Orleans, many pilots and crew of flatboats and keelboats traveled by the Trace overland to their homes in the Ohio River Valley. (Given the strong current of the Mississippi River, it was not until steam-powered vessels were developed in the 1820s that travel northward on the river could be accomplished by large boats.) The Natchez Trace also played an important role during the War of 1812. Today the modern Natchez Trace Parkway, which commemorates this route, still has its southern terminus in Natchez.

In the middle of the nineteenth century, the city attracted wealthy Southern planters as residents, who built mansions to fit their ambitions. Their plantations were vast tracts of land in the surrounding lowlands along the river fronts of Mississippi and Louisiana, where they grew large commodity crops of cotton and sugarcane using slave labor. Natchez became the principal port from which these crops were exported, both upriver to Northern cities and downriver to New Orleans, where much of the cargo was exported to Europe. Many of the mansions built by planters before 1860 survive and form a major part of the city's architecture and identity. Agriculture remained the primary economic base for the region until well into the twentieth century.

During the American Civil War Natchez was surrendered by Confederate forces without a fight in September 1862. Following the Union victory at the Battle of Vicksburg in July 1863, many refugees, including former slaves, freed by the Emancipation Proclamation, began moving into Natchez and the surrounding countryside. The Union Army officers claimed to be short on resources and unable to provide for the refugees. The Army planned to address the situation with a mixture of paid labor for freed slaves on government leased plantations, the enlistment of able bodied males who were willing to fight in the Union Army and the establishment of refugee camps where former slaves could be provided with education. However, as the war continued, the plan was never effectively implemented and the leased plantations were crowded, poorly managed and frequently raided by Confederate troops who controlled the surrounding territory. Hundreds of people living in Natchez, including many former slaves and refugees, died of hunger, disease, overwork or were killed in the fighting during this period.

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