Biodiversity in aquatic ecosystems is generally viewed as a reliable indicator of ecosystem health. High biodiversity indicates a healthy ecosystem that functions properly because of the right combination of physical, chemical, and biological factors. Anthropogenic disturbance decreases biodiversity by modifying these factors. The Grande Ronde and Imnaha River basins in northeastern Oregon are occupied by land uses that could be disturbing aquatic ecosystems. Biological assessments (bioassessments) were used in this study to determine the effects of disturbance on macroinvertebrate community structure within the Grande Ronde, Wallowa, and Imnaha rivers. Macroinvertebrate distribution and abundance data collected from upstream and downstream sites on each river were used to calculate species- and community-level metrics (e.g., richness, abundance and the Family Biotic Index [FBI]) for each site. These metrics revealed differences between sites and between rivers, as well as a decrease in water quality and biodiversity for the Grande Ronde and Imnaha rivers. The Wallowa River did not conform to this trend, likely because the upstream site was directly below an oligotrophic lake. In general, metrics were not indicative of impaired macroinvertebrate communities, but management efforts should be taken to conserve biodiversity in lower reaches of rivers within the Grande Ronde and Imnaha river basins.