Completion of the current 9-foot navigation project (1938-1942) using a series of low-head dams had a tremendous ecological impact on the Upper Mississippi River, and the refuge. This system of 26 locks and dams (11 on the refuge) changed the previously free-flowing river to a series of shallow reservoirs from St. Louis, Missouri, to Minneapolis, Minnesota.
For several decades, the newly created pools supported a wealth of fish, wildlife, and aquatic habitats. However, typical of dammed river systems, the initial productivity of the pools diminished significantly over time. Although water level management of the pools changed some over the years, the defining purpose for water level management was, and is, to ensure navigation pool water depths for a commercial navigation channel. The result is a deeper, relatively stabilized water system, especially during the summer.
Changing the free-flowing river to a series of reservoirs, and stabilization of water levels, over time, adversely affected the biological resources of the river, and thus the refuge. Among the principal results have been a reduction in seasonal mudflat/sandbar areas and a significant decline in aquatic plant community abundance, diversity, and distribution. Fish and wildlife dependent on these plant communities have also declined, and/or moved elsewhere.