Alphabetically
- Arrow Rock, Missouri
- Augusta, Missouri
- Atchison, Kansas
- Bellevue, Nebraska
- Bismarck, North Dakota
- Black Eagle, Montana
- Boonville, Missouri
- Bridgeton, Missouri
- Brockton, Montana
- Brownville, Nebraska
- Cannon Ball, North Dakota
- Carter Lake, Iowa
- Cascade, Montana
- Chamberlain, South Dakota
- Chamois, Missouri
- Chesterfield, Missouri
- Council Bluffs, Iowa
- Culbertson, Montana
- Dakota City, Nebraska
- Decatur, Nebraska
- Defiance, Missouri
- Elwood, Kansas
- Fort Benton, Montana
- Fort Peck, Montana
- Fort Pierre, South Dakota
- Fort Thompson, South Dakota
- Fort Yates, North Dakota
- Frazer, Montana
- Gasconade, Missouri
- Glasgow, Missouri
- Great Falls, Montana
- Hermann, Missouri
- Independence, Missouri
- Jefferson City, Missouri
- Kansas City, Kansas
- Kansas City, Missouri
- Lansing, Kansas
- Leavenworth, Kansas
- Lexington, Missouri
- Loma, Montana
- Lower Brule, South Dakota
- Lupus, Missouri
- Mandan, North Dakota
- Matson, Missouri
- Miami, Missouri
- Missouri City, Missouri
- Mobridge, South Dakota
- Napoleon, Missouri
- Nebraska City, Nebraska
- New Haven, Missouri
- Niobrara, Nebraska
- North Kansas City, Missouri
- Oacoma, South Dakota
- Omaha, Nebraska
- Parkville, Missouri
- Pick City, North Dakota
- Pickstown, South Dakota
- Pierre, South Dakota
- Plattsmouth, Nebraska
- Poplar, Montana
- Riverdale, North Dakota
- Riverside, Missouri
- Rocheport, Missouri
- Rulo, Nebraska
- St. Albans, Missouri
- St. Charles, Missouri
- St. Joseph, Missouri
- Santee, Nebraska
- Sibley, Missouri
- Sioux City, Iowa
- South Sioux City, Nebraska
- Springfield, South Dakota
- Stanton, North Dakota
- Sugar Creek, Missouri
- Toston, Montana
- Townsend, Montana
- Ulm, Montana
- Washburn, North Dakota
- Washington, Missouri
- Waverly, Missouri
- West Alton, Missouri
- White Cloud, Kansas
- Wildwood, Missouri
- Williston, North Dakota
- Wolf Point, Montana
- Yankton, South Dakota
Read more about this topic: List Of Populated Places Along The Missouri River