Springs are essential sources of water for humans and wildlife in the Sonoran Desert and, despite their isolation, they often support diverse aquatic communities. However, flows in these systems are declining due to groundwater pumping and increasing temperatures and aridity. In the western Sonoran Desert, two spring-fed systems represent the vast majority of perennial surface water along the U.S.-Mexico border: Quitobaquito, an upland hillslope spring, and a nearby spring-fed reach of the Rio Sonoyta. In this study, we quantified how aquatic invertebrate species richness and community composition varied by habitat type and season at these two sites. We found that habitat was a significant driver of composition for both sites, but seasonal variation was only influential for species richness in the Rio Sonoyta. Continued declines in flow will likely lead to significant losses of aquatic invertebrate biodiversity at both sites.