The campground at Missouri Headwaters State Park  (four miles northeast of Three Forks on Road 286, 406/994-4042, http://fwp.mt.gov/parks/ , May 1–Sept. 30, $12 camping fee includes day use) has brushy riverside sites perfect for those on a Lewis and Clark pilgrimage. Read their journals first if you doubt the importance of bringing mosquito repellent.
There’s also a large state park campground (with showers) at Lewis and Clark Caverns (19 miles west of Three Forks on Hwy. 2, 406/287-3541, http://fwp.mt.gov/parks/ , $15 camping May–Sept., $13 Oct.–Apr., $40 cabin May–Sept., $25 Oct.–Apr.).
From Norris, about 30 miles south of Three Forks , head east on Highway 84 for nine miles to find Red Mountain (406/683-2337, www.blm.gov/mt/ , May–Dec., $8), a Bureau of Land Management campground near the bridge over the Madison River.
For a secluded spot, try Potosi (about eight miles south of Pony, 406/682-4253, June–Sept., free).