Others with more local knowledge than I will have better advice, but if I'm not mistaken, that stretch of water is pretty silty, and will soon plug most backpacking pump/filters.
Veterans of that trip have suggested:
a. carrying your own water, as you may be planning
b. carrying an empty 5-gal bucket which you fill at the end of each day and let settle overnight, then pump/filter in the morning
c. filtering river water with a cloth vacuum-cleaner bag
d. use powdered alum to quickly remove the silt from river water:
Let us know how you fare; that river trip is on my list!
In fact, a few years ago, my wife and I drove about 40 miles along that stretch of river on the Missouri Breaks Backcountry Scenic Byway in our VW Camper van. Had lunch at Woodhawk Bottom, which we were told was a Lewis & Clark campsite:
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