The Red River expedition of 1806 was the first major scientific probe into the American West to be led by civilian scientists and include an academically trained naturalist. As part of his master plan for the exploration of the West, President Thomas Jefferson considered the Red River expedition second in importance only to Lewis and Clark's investigation of the Missouri and Columbia rivers. Though it was billed as a scientific survey, the Red River expedition had strong commercial and diplomatic overtones and became both an element in the boundary dispute with Spain and a source of embarrassment for the Jefferson administration as the Burr conspiracy unfolded. By sending an American force up the Red River Jefferson hoped to confirm reports that the Red might provide a commercially viable watercourse to Santa Fe, to woo the region's Indians to the American camp, and to test the Louisiana Purchase's disputed western border with New Spain.
Secretary of War Henry Dearborn and Natchez scientist William Dunbar were responsible for directing the expedition. Planning for the mission, which Jefferson called his "Grand Excursion" to the Southwest, began in 1804, and Dunbar made a trial reconnaissance up the Ouachita River during the winter of 1804–05. Extensive personnel searches produced Thomas Freeman, an experienced astronomer and surveyor, as field leader and Peter Custis, a medical student at the University of Pennsylvania and protégé of noted naturalist Benjamin Barton Smith, as naturalist and ethnographer. Capt. Richard Sparks, a forty-five-man military contingent, and French and Indian guides were employed to escort the civilian scientists in their ascent of the Red. Congress appropriated $5,000 for the Red River expedition in 1805, and by late April 1806, when the contingent left Natchez, expenses had grown to $11,000, or three times the original funding of Lewis and Clark.
The dream of tracing a water route to the southern Rockies and winning the Indians to the American side was cut short by political machinations culminating in armed Spanish intervention. Hoping to provoke an international confrontation for personal gain, James Wilkinson had informed Spanish officials of the American designs on the Red River area. While the Americans poled their way up the river, two Spanish military expeditions marched to intercept them. Freeman and Custis entered the Red River on May 2, 1806, and left Natchitoches on June 2. They were 615 miles up the river on July 28, when they met a Spanish force under the command of Francisco Viana, who ordered them to turn back. By August 1 the Americans were heading down the river. The expedition's turning point in what is now Bowie County, Texas, is still known as Spanish Bluff.
Though the expedition's failure caused political embarrassment for the Jefferson administration, the bloodless confrontation between American explorers and Spanish troops failed to trigger the war that Wilkinson and Aaron Burr had hoped for. The diplomatic uproar caused Spain to pursue a less confrontational policy, which effectively opened up the Red River country to American traders. Diplomatic tensions resulting from the Red River episode persuaded Jefferson to abandon an excursion up the Arkansas River that had been planned for 1807. The scientific achievement of the Red River expedition was overshadowed by the more dramatic discoveries of Lewis and Clark and obscured in the controversy over the expedition's premature termination. The principal lasting contributions of the Red River expedition were the documents left by its leaders. As records of nineteenth-century scientific exploration, Freeman's journal and Custis's natural history catalogues provide valuable information on the Indian life and ecology of the Red River.