Winds often blow up the river valley. Wind speeds can at times be greater on the river than reported for surrounding land areas, due to the fetch offered by the open river. An upriver wind can slow your progress down the river substantially. Be prepared to factor this wind effect into your trip planning. It is not unusual for a canoe to have to be "worked" down the river, regardless of current, as a result of a strong upriver wind.
Another weather factor to consider is fog. Any time of year a fog can build up on the river. This is especially pronounced in the evenings and mornings of autumn. It is not unusual to wake up on a sandbar and find the river socked in with fog. In such an event, you will have to wait several hours for the fog to clear before you can safely get underway. Traveling the river in a heavy fog would be a folly and should not be attempted. It is a good idea to factor this into your trip planning and allow a time cushion for overnight trips, in the event you are fogged in one morning.
Severe weather can be a major factor on any open body of water. The Missouri River is a big wide open river and is more like a lake in this respect. A Missouri River paddler needs to take the same weather precautions that apply to lake or ocean travel. Please review the safety section for more information. The water trail maps have a weather button you can activate for local weather near your section of river. You can also access a long range forecast at http://www.weather.gov/forecastmaps