We collected over 500 zoobenthic samples over a 4-month period in summer 2007. Dominant invertebrate taxa were chironomids, ceratopogonids, and oligochaetes. Flow pulses significantly changed sandbar shape, altered substrate composition, and changed the number of channels. Invertebrate richness and community composition were tied to river channel complexity rather than hydrology. Downstream displacement of organisms was more complete in areas of high hydraulic stress (leading edge of bars), whereas areas of flow relief were more stable. Additionally, community composition of a side channel alternated between side channel and backwater assemblages when it was repeatedly cut off and reopened. Understanding roles of hydrogeomorphic fluctuations continues to be important, especially with climate models predicting increased precipitation variability in the Great Plains.