On August 31, 1803, Meriwether Lewis left Pittsburgh in his newly completed keelboat, heading down the Ohio with perhaps eleven men. Impeded by low water, he took nearly a month to reach Cincinnati. About October 15 he reached Clarksville, Indiana Territory, just below the Falls of the Ohio, where William Clark awaited him. There they gained several recruits, chiefly young Kentucky woodsmen gathered in by Clark, and York, Clark's black slave. Leaving Clarksville on October 26, they recruited two or three men at Fort Massac (present Illinois) on November 11 and 12, including hunter and interpreter George Drouillard and Private Joseph Whitehouse, one of the expedition's journalists.

At the mouth of the Ohio, which they reached on November 14, they spent a week mapping and measuring and taking celestial observations, then started up the Mississippi on November 20. On their left hand now was present-day Missouri, part of the Louisiana Purchase, still under the rule of Spanish officials pending the transfer to the United States the following spring. On November 28, Lewis left Clark in charge of the boat and the men at the mouth of the Kaskaskia River and proceeded by land to St. Louis to confer with the Spanish authorities. He found them by no means pleased by the expedition; they requested that he make his winter camp on the American side of the river, pending the transfer of Louisiana. Clark proceeded upriver, met and conferred with Lewis on December 9, then left his partner at St. Louis and moved to the American side near the mouth of the River Dubois in modern Illinois. There on December 13 he established the camp where the Corps of Discovery awaited the coming of spring to begin the trip up the Missouri.

During the five months at Camp Dubois the captains gathered further recruits, some of them frontiersmen who enlisted especially for the expedition, others army enlisted men from various western garrisons who were assigned to the expedition by their commanding officers. The long and inevitably tedious winter enabled the captains to evaluate their men, to weed out a few undesirables, and to introduce the more undisciplined to the rigors of army regimen. During the wait they were also able to gather much knowledge about the Missouri River and its native peoples from the fur traders and river men of the region, in particular James Mackay, and to acquire copies of John Thomas Evans's maps of the river. The transfer of Louisiana to the United States was formally accomplished in March 1803, and spring soon brought weather suited for travel.

Lewis was in St. Louis when Clark left Camp Dubois on May 14, 1804, with the keelboat and two pirogues, manned by perhaps 42 men. The party arrived at St. Charles on the Missouri on May 16, and Lewis joined them on the twentieth. At St. Charles they added a few more boatmen and set out on the afternoon of May 21.

The journey up the Missouri, against the current, was slow and laborious; occasionally they could sail with a favorable wind, but more often they poled upstream or the men pulled the boats with a tow rope, walking on the shore. They soon left the last white settlements behind and began to exercise more caution as they entered Indian country. Several times they met fur traders headed down river with their pelts, having wintered among one tribe or another. One of them, Pierre Dorion, Sr., the captains hired to return upstream with them as an interpreter.

Toiling along in the increasing summer heat, plagued by boils, diarrhea, mosquitoes, and sandbars, the Corps of Discovery reached the mouth of the Kansas River, the future site of Kansas City, on June 26. Almost another month was required to reach the mouth of the Platte, on July 21. Just above the Platte they established Camp White Catfish, on the present Iowa shore, and rested a few days (July 22-26). On July 30 they reached a high bluff near the river in modern Nebraska, which they would call Council Bluff, for there they had their first council with the chiefs of the Otos and Missouris, informing them of the change in sovereignty in Louisiana; they remained at the bluffs until August 2.

Some disciplinary problems marred their progress; unauthorized tapping of the whiskey supply earned Private John Collins one hundred lashes. More serious was the desertion of Private Moses B. Reed and the boatman La Liberté in early August; Reed was captured, forced to run the gauntlet, and officially expelled from the party, though he remained with them for the time being because he could not be abandoned in the wilderness. La Liberté made good his escape.

A loss of a different sort soon followed. Just after a second council with the chiefs of the Otos in northeast Nebraska, Sergeant Charles Floyd died, probably of a ruptured appendix, at the present site of Sioux City, Iowa. His comrades buried him on a bluff on the Iowa shore, naming a nearby stream Floyd's River. He would, in fact, be the only man to die on the expedition, but this must have seemed too much to hope for at the time. Four days later they reached the Vermillion River, in present South Dakota, 112 days and about 860 miles out from Camp Dubois.