Well I guess we know where you stand. 
The lock and dam system of navagation is composed of something like 27 L&Ds.  They are from St Louis North. 
Don't know or care if they hold back the Missouri or not.but since the Missouri dumps into the Miss at St Louis I would guess not. 
Now are you talking about that other big river that was known to be 1 mile wide and an inch deep? Now I believe that was before the Corps channeled it. And those bodies of water , are they natural lakes or just impoundments? You know for flood control.
I've got to admit that I don't know much about the Missouri but doesn't the whole west have a drought problem or is it just Montana  and the Dakotas?
The lower Mississippi apparently doesn't need more water to run barges or the Corps would have built more L&Ds. 
I checked record water levels at Cape Girardo Missouri and found that in 1909, before the L&Ds the record low water level was .6 feet. 
So that tells me that low water levels are nothing new to the rivers and since cape Girardo is below the L&D system the Missouri river must not have had much water in it either. 
This is spring time.  The time for floods. 
I checked the Missouri river levels in the Kansas city area, the only district that the Missouri runs through where I could find records and found you guys are as much as 6 feet below flood level and as I said before its the time for floods. 
I think your concerns are probably founded but i have to question your target.
Here is where I got my information 
http://www2.mvr.usace.army.mil/Water...new/layout.cfm