Off-channel habitats such as backwaters and side channels provide important nursery and feeding habitats for native fishes of the Missouri River, including the endangered pallid sturgeon (Scaphirhynchus albus). We mapped backwaters, side channels, and secondary channels (henceforth referred to as other channels) on the Missouri River between Fort Peck dam and the North Dakota state line for 1956/57, 2009, and 2011, the latter of which was a flood year. We compared the total number of mapped features and mean length, area, and perimeter of the features between 1956/57 and 2009. Each habitat type increased significantly in total number between 1956/57 and 2009. Although we observed an increase in the total number of off-channel habitats between 1956/57 and 2009, the average area of each type of habitat decreased by 50%, which suggests that these areas may be unsuitable for the pallid sturgeon and other native fishes of the Missouri River below Fort Peck dam. A large flood event in 2011 may have been a significant enough event to restore these habitats; examination of post-flood imagery may help answer that question and guide restoration and recovery efforts for the pallid sturgeon.