The impacts of human activities on the ecosystem have resulted and continue to result in a decline in the environmental quality of the Upper Mississippi River System (UMRS).

The resource impacts include backwater and secondary channel sedimentation, altered hydrology, loss of connectivity of the floodplain to the river, impeded fish migration, loss of island habitat, endangered plant and animal species, and loss of native plant community diversity and abundance.

Large increments of ecosystem decline can be attributed to the construction and operation of the navigation system, but there are many ecological stressors contributing to ecosystem degradation including land use changes, floodplain development, exotic species, sedimentation resulting from land use practices, construction of the levee system, and nonpoint source pollution.

The primary authority available to the U.S. Army Corps of Engineers to address this decline is the Upper Mississippi River Restoration - Environmental Management Program (UMRR-EMP), established by the Water Resources Development Act of 1986. The Upper Mississippi River - Illinois Waterway System Navigation Feasibility Study concluded that the UMRR-EMP and national program authorities, and the limited environmental management activities available under a single-purpose navigation project, have been insufficient to meet the environmental needs on the UMRS.

Degradation of the system will continue in the future in the absence of any additional federal action.