Major ground-water quality issues in the Lower Illinois River Basin include nutrients and agricultural chemicals, and trace elements. The Illinois River is a primary channel for the transport and disposal of much of the State's human, animal, industrial, and agricultural wastes. Alluvial aquifers underlying the Illinois River supply large amounts of drinking water. Contaminants in the river can move into the alluvium and into the water-supply wells. Also, the major bedrock valley aquifers are hydraulically connected to the Illinois River alluvium. Withdrawals from these buried aquifers can potentially draw in contaminated river water.

Results from recent statewide studies indicated that concentrations of nitrate and other agricultural chemicals exceeded maximum contaminant levels (MCLs) for drinking water in surface- and ground-water supplies. In 1990, about 9-million pounds of atrazine were applied in Illinois, nearly one-sixth of the national total and more than any other State. Results from several recent studies of ground-water quality in public-supply wells throughout Illinois have indicated concentrations of nitrate, pesticides, and volatile organic compounds above MCLs for safe drinking water.