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The stream ecosystem reflects physical, chemical, and biological characteristics of a watershed. Many of these characteristics are assessed during the Surface Water and the Bed-Sediment and Fish Tissue NAWQA studies. The health of stream biotic communities and the condition of physical habitat are evaluated in ecological studies.

Major water-quality issues in the study area include sedimentation, toxic substances in sediment, elevated concentrations of nutrients and agricultural chemicals, low concentrations of dissolved oxygen in streams, and the introduction of exotic species to the basin.

Dissolved oxygen is needed to support aquatic life. Many wastes, such as domestic and industrial wastes, discharged to the Illinois River produce ammonia nitrogen and consume oxygen, resulting in seasonal low concentrations of dissolved oxygen. Reduced dissolved oxygen concentrations also have affected the diversity of species in backwater lakes. The aquatic life and vegetation compete with sediments and pollutants for available dissolved oxygen.

Zebra mussels (an exotic species) compete with native mussel species, create operational problems for hydraulic structues and water intakes, and affect the supply of dissolved oxygen in rivers and streams. Zebra mussels can reach tremendous densities. During the Great Mississippi River Flood of 1993, the Illinois Natural History Survey recorded up to 61,000 zebra mussels per square meter near the confluence of the Illinois and Mississippi Rivers.