The enlisted men who volunteered for the Expedition brought along their own stands of arms – smoothbore muskets manufactured at Springfield (1795 and on) or Harpers Ferry armories (1801 and on), cartridge boxes and bayonets, as well as pipe tomahawks. Lewis procured 15 rifles from the Harpers Ferry Armory in 1803, but a recent article in the National Rifle Association’s magazine calls into question whether these rifles were the Harpers Ferry 1803 model. It seems more likely from this recent research that the rifles were leftovers from the Anthony Wayne period, "Model 1792s" in storage at the armory. These rifles were longer, full-stocked and smaller caliber weapons than the 1803s, none of which are recorded in official records as being manufactured before 1804, too late to join the Expedition.

Some of the men from Kentucky may have brought their own long "Pennsylvania" Rifles along. We know that William Clark had a "handsome fuzee" he lost in the freshet (gully-washer) along the Missouri River near Great Falls. A "fuzee," or fusil was a lightweight, shorter weapon, sometimes smoothbore but other times rifled, and sometimes finely decorated with brass ornamentation. Lewis may also have had a fusil, certainly had his air gun, and also had a brace of pistols he purchased in Philadelphia.

Both officers as well as the three sergeants would have carried swords as symbols of their rank. These were short, curved swords of simple design for the sergeants and more elaborate, personal weapons for the officers. There were no officially prescribed sword patterns for officers during the period. The officers were also supposed to carry spontoons, and we know from the journals that both Lewis and Clark did, even in the rough country along the Missouri in Montana. A spontoon is a long (about seven feet) pole with a spear and crossbar on the end of it. The spontoon patterns were simple and not showy during the period, with a simple spear point and crossbar on an undecorated haft. Spontoons were used in ranks of soldiers on the battlefield as a sign of rank, a place enlisted men could look for guidance. They were sometimes used to straighten ranks of men by holding them horizontally alongside the line.