Droughts are unpredictable disturbances characterized in streams by declining flow, reduced habitat availability, and deteriorating abiotic conditions. Such events typically reduce benthic invertebrate taxon richness and modify assemblage composition, but little is known about how hyporheic invertebrate assemblages respond to drought or how these responses relate to changes in benthic assemblages. We hypothesized that taxon richness (diversity) and variability (as within-site diversity) in benthic assemblage composition would decline as drought proceeded, whereas concurrent changes in hyporheic assemblages would be lower in this more stable environment. We predicted that benthic assemblage composition between sites would converge as epigean taxa were selectively eliminated, whereas between-site hyporheic diversity would change little. We sampled benthic and hyporheic invertebrates concurrently from 4 sites along a groundwater-fed stream during the final stages of a severe supraseasonal drought punctuated by a record heat wave. Abiotic conditions in benthic habitats deteriorated as flow declined, but changes were less pronounced in the hyporheic zone. Benthic diversity declined during drought, whereas hyporheic diversity changed little. However, benthic within-site diversity increased as the drought progressed because of localized variation in the abundance of common taxa. Temporal trends in hyporheic diversity were less consistent. Benthic assemblages at individual sites became more similar, especially during the heat wave, reflecting low diversity and abundance. Hyporheic assemblages changed markedly because of temporary increases in abundances of epigean and hypogean amphipods. These contrasting responses of benthic and hyporheic assemblages to drought should be recognized when developing management strategies for drought-impacted streams