Boating is very popular at Lewis and Clark SRA. Sailboats, speed boats and personal watercraft are all permitted. Fuel is available at the Weigand Marina. The area offers 116 leased seasonal dock slips and 10 daily rental dock slips that may be reserved in advance. Four ramps are available in the Weigand area. A portion of the spillway and the tailrace of Gavins Point are no-wake zones.

The lake also offers access to the Missouri River. Those interested in boating or fishing on the River are encouraged to view the interactive Missouri River Outdoor Recreation Access Guide, which shows public access sites for fishing, hunting, boating, camping and more. It also serves as a navigation guide.