Although titled Mississippi..., the starting point is in the glacially carved St. Croix Valley above its confluence with the Mississippi. One follows either side of the river valley to the point where the St. Croix merges with the Mississippi on the Minn./Wisc. border.
The Mississippi, already a large river from its convergence with the Minnesota River below Minneapolis/St. Paul, now is the large, deep river that cuts through high bluffs and cliffs all the way down to Dubuque, Iowa.
Simply follow either side of the valley (at best alternating at bridge crossings along the way)and picking routes that local maps show to be the most scenic (although most maps show both sides as scenic!). Fall foliage season is an ideal time with cooler, drier weather and magnificent color. Once in Dubuque (at two-day trip, at best) I find a direct route south to southernmost Iowa (Keokuk) the best as the river scenery lessens until one reaches Missouri.