Aquatic macroinvertebrates are sensitive to changes in their chemical and physical environment, and as such, serve as excellent indicators of overall ecosystem health. Moreover, temporal and spatial differences in macroinvertebrate community structure can be used to investigate broad issues in aquatic science, such as the hypothesis that changes in climate are likely to have disproportionately large effects on small, intermittent stream ecosystems. We quantified macroinvertebrate community structure and abiotic conditions at ten stream sites with different dominant hydrologic regimes in the Colorado Plateau, ranging from small, intermittent desert streams to large perennial mountain rivers. Considerable differences were observed in community structure between sites with differing hydrologic regimes. Quantitative results of non-metric multidimensional scaling (NMDS) ordination and Spearman rank correlations between physical habitat and macroinvertebrate resemblance matrices indicate that discharge, geomorphic channel unit type (% pools vs. % riffles), percent of substrate composed of sand, and velocity were the subset of measured habitat variables that best explained the differences in macroinvertebrate community structure among sites. Of the 134 taxa identified, nine taxa explained 95 % of the variability in community structure between sites. These results add to a growing base of knowledge regarding the functioning of lotic ecosystems in the Colorado Plateau, and provide timely information on anticipated changes in the structure and function of aquatic ecosystems in response to predicted future environmental conditions.