Posting to this topic to update it.
Link to ACOE navigational charts has changed to this
http://www.mvr.usace.army.mil/Missions/Navigation/NavigationCharts/UpperMississippiRiver.aspx
Also…some small lakes that are part of those Mississippi River pools can be found by using the MNDNR Lakefinder.
http://www.dnr.state.mn.us/lakefind/index.html
For example, checking Dakota County (Hastings)…
http://www.dnr.state.mn.us/lakefind/search.html?name=&county=19
Lake Rebecca has a depth map
http://www.dnr.state.mn.us/lakefind/lake.html?id=19000300
There are others too…you gotta search by County.
Finally, the Navionics webapp shows depths for the River.