Section 1 of the Lewis & Clark Bicycle Trail begins near the 1803-04 winter encampment of the Corps of Discovery. In Missouri, 151 miles of this route is on the Katy Trail, a crushed limestone trail built on an abandoned railroad bed next to the river. If this surface is not to your liking, the Jefferson City Option offers a hilly, paved alternate reducing the number of miles on limestone. The route also uses the Steamboat Trace in Nebraska, another crushed limestone trail. The bustle of traffic of metropolitan Kansas City is avoided, but be prepared for hills whenever the route leaves the river valley. This section ends at the Iowa West Trailhead in Council Bluffs, a bicycling-friendly community with a network of cycling paths throughout the city.

Major funding for the Lewis & Clark Bicycle Trail has been provided by REI.