The Navigation and Ecosystem Sustainability Program comprises projects on the Upper Mississippi River and Illinois Waterway navigation system and lies within portions of Illinois, Iowa, Minnesota, Missouri, and Wisconsin.

The Upper Mississippi River navigation system extends from the confluence with the Ohio River, River Mile 0.0, upstream to the Upper St. Anthony Falls Lock in Minneapolis-St. Paul, Minnesota, river mile 854.0. The Illinois Waterway navigation system extends from its confluence with the Mississippi River at Grafton, Illinois, river mile 0.0, upstream to the T. J. O’Brien Lock in Chicago, Illinois, river mile 327.0. The System contains 1,200 miles of nine-foot deep channels, 37 lock and dam sites and thousands of channel training structures.

The Upper Mississippi River and Illinois Waterway ecosystem includes the river reaches described above, as well as the floodplain habitats that are critically important to large river floodplain ecosystems. The total acreage of the river-floodplain system exceeds 2.5 million acres of aquatic, wetland, forest, grassland, and agricultural habitats.