The increased variation in climate in the southwestern United States is leading to dramatic fluctuations in stream discharge, including atypical large floods and long-term droughts. These hydrological changes will have impacts on aquatic biota, including aquatic invertebrates. Examining these impacts can be challenging due to the presence of confounding factors. However, streams in national parks are ideal for study because they are protected from most confounding anthropogenic disturbances. We studied changes in macroinvertebrate community structure in five national parks using a 10-year biomonitoring dataset (2012 to 2022). Macroinvertebrate data were collected from riffles in perennial streams in the Sonoran Desert and Southern Plains ecoregions. We found a total of 193 invertebrate taxa, including a total of 73 EPT taxa. Most parks had distinct communities, except for Montezuma Castle National Monument (MOCC and MOWE) and Tuzigoot National Monument, which are in the same larger Verde River watershed and were compositionally similar. Average EPT taxonomic richness was highest at Pecos National Historical Park (PECO) and MOCC with 18 taxa, and lowest at Tumacácori National Historical Park (TUMM) with 3 taxa, which does receive treated wastewater inputs from an urban area 24 kilometers upstream. Across the time period, we found that all parks had weighted tolerance values (TV) generally ranging from 4 to 6 (representing very good to fair water quality, respectively), with the lowest tolerance values at PECO and the highest values at TUMM. TUMM had a TV peak of 7.3 in 2015, which was related to a large increase in density of snails in the genus Physa following an extraordinary flood event. The variation in TV throughout the 10-year period is part of the communities’ responses to changes in flow and habitat. Further analyses, including IBIs and statistical modelling of species abundances, will clarify these community responses to flow changes.