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In June 1995, heavy rains caused severe flooding and massive debris flows on the Staunton River, a 3(rd)-order stream in the Blue Ridge Mountains (Virginia, USA). Scouring caused the loss of the riparian zone and repositioned the stream channel of the lower 2.1 km of the stream. Between 1998 and 2001, we conducted seasonal macroinvertebrate surveys at sites on the Staunton River and on White Oak Canyon Run, a reference stream of similar size and geology that was relatively unaffected by the flood. Our study was designed to determine the extent to which flood-induced changes to the stream channel and riparian habitats caused long-term changes to macroinvertebrate community structure and composition. Sites within the impacted zone of the Staunton River supported diverse stable benthic macroinvertebrate assemblages 3 y after the flood despite dramatic and persistent changes in environmental factors known to be important controls on stream ecosystem function. However, significant differences in total macroinvertebrate density and trophic structure could be attributed to the flood. In autumn, densities of most feeding guilds, including shredders, were higher at impacted-zone sites than at all other sites, suggesting higher overall productivity in the impacted zone. Higher shredder density in the impacted zone was surprising in light of expected decreases in leaf-litter inputs because of removal of riparian forests. In contrast, in spring, we observed density differences in only one feeding guild, scrapers, which showed higher densities at impacted-zone sites than at all other sites. This result conformed to a priori expectations that reduced shading in the impacted zone would lead to increased light and higher instream primary production. We attribute the seasonal differences in trophic structure to the effects of increased temperatures on food quality and to the relationship between the timing of our sampling and the emergence patterns of important taxa.