The influence of specific stressors, such as nutrient enrichment and physical habitat degradation, on biotic integrity requires further attention in Midwestern streams. We sampled 53 streams throughout Illinois and examined relationships between macroinvertebrate community structure and numerous physicochemical parameters. Streams were clustered into four major groups based on taxa dissimilarity. Habitat quality and dissolved nutrients were responsible for separating the major groups in a nonmetric multidimensional scaling ordination. Furthermore, the alignment of environmental factors in the ordination suggested there was a habitat quality-nutrient concentration gradient such that streams with high-quality habitats usually had low concentrations of nutrients. Discrimination by community measures further validated the major stream groups and indicated that forested streams had generally higher biological integrity than agricultural streams, which in turn had greater integrity than urban streams. Our results demonstrate that physical habitat degradation and nutrient pollution are important and often confounded determinants of biotic integrity in Illinois streams. In addition, we suggest that management of Midwestern streams could benefit from further implementation of multivariate data exploration and stream classification techniques.