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Extreme disturbances eliminate aquatic biota and alter community structure and function. During a supraseasonal drought in north-central Texas in the summer and fall 2006, macroinvertebrate communities from persistent groundwater-dependent macrohabitats of varying hydrology and riparian shading were investigated to study their role as invertebrate refugia, and to characterize the taxonomic and functional community structure of benthic assemblages. Ash Creek was the only stream with surface flow within a 35-km radius during the drought. Two perennial and three intermittent stream sites were studied that included perennial riffles, a perennial pool, shaded disconnected pools, and disconnected pools in full sun. Riffles had significantly higher taxa richness, EPT (Ephemeroptera, Plecoptera, and Trichoptera) richness, proportion of lotic taxa, and diversity than other macrohabitats. Macrohabitats were refugia for 106 benthic macroinvertebrate taxa, and perennially flowing habitats contained 19 taxa (17.9% of total taxa) not collected in disconnected pools. Larvae and pupae of caddisflies Marilia spp., Oecetis spp., Helicopsyche spp., and riffle beetle Microcylloepus spp. larvae and adults demonstrated resistance to drought by their presence in shaded disconnected pools without surface flow for over a month. Gathering-collectors were the most dominant and taxonomically diverse functional feeding group (FFG) in all macrohabitats. Scrapers ranked second in dominance in riffles, followed by predators; however, predators were the second most dominant FFG in all pool habitats. Continued overabstraction of groundwater in the region could lead to loss of perennial riffles and pools and extirpation of lotic taxa, such as Lutrochus spp., Mayatrichia spp., and Marilia spp., and dramatically alter community structure and function.