Despite the widely accepted importance of the hyporheic zone as a habitat for stream macroinvertebrates during floods, few data exist regarding community composition and distribution during periods of low flow or drought in perennial streams. Integrating research on hyporheic invertebrates with results from a long-term study of a UK river provided the opportunity to examine how benthic and hyporheic macroinvertebrate communities respond to inter-annual variability in river flow and periods of groundwater drought. Changes in the riverine macroinvertebrate community associated with low flow included a reduction in species richness and the number of individuals per sample, particularly aquatic insects. The hyporheic community was characterized by a relatively homogeneous composition during a period of severe low flow, punctuated by short-term changes associated with variation in water temperature rather than changes in discharge. We present a conceptual model of the processes influencing benthic and hyporheic invertebrates under low-flow conditions. Previous studies have seldom integrated these two assemblages and their interactions. The model presented highlights the potential importance of surface water and hyporheic zone linkages for riverine invertebrate communities under a range of flow conditions.