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The natural flow regime of rivers has been altered throughout the world in a variety of ways, with many alterations resulting in reduced flows. While restoring impaired systems remains a societal imperative, a fundamental understanding of the effects of reduced flows on river ecosystem structure and function is needed to refine restoration goals and guide implementation. We quantified the effects of chronic low flows on snag-dwelling macroinvertebrate community structure and production in a low-gradient river. Macroinvertebrates commonly associated with flowing water (e.g. passive filter-feeders (PFF)) and higher quality habitats (e.g. Ephemeroptera, Plecoptera and Trichoptera (EPT)) had significantly higher abundance and biomass, and showed trends of higher production, in faster flowing reaches upstream of a hydrologic disconnection created by a drainage ditch. The presence of EPT and PFF groups resulted in a significantly more diverse community composed of larger-sized individuals compared with downstream, low-flow reaches, where smaller-bodied taxa (e.g. small crustaceans), and groups reflective of degraded conditions (e.g. Oligochaeta, Isopoda and Chironomidae) dominated production. Multivariate analyses suggested that differences between these two disparate communities were driven by water velocity and organic matter resources. Mean estimates of total community production did not differ significantly between the two reaches, however, there were areas in low-flow reaches that attained high secondary production because of patchily distributed and highly productive chironomids. Results demonstrate that long-term reductions in flows, even in a low-gradient river, can lead to significant shifts in macroinvertebrate communities, ultimately influencing energy flow pathways in stream food webs. Copyright © 2015 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]