The inter-annual variation in the structure of the benthic community of riffles and pools was evaluated in contrasting geomorphic settings. The community structure of riffles and pools was a function of habitat, reach gradient, and discharge and was taxon specific. In years of below average peak discharge, riffles had higher taxon richness than pools (66 versus 47) but richness was similar between habitats during a year of average discharge (56 versus 54). The percentage composition of oligochaetes and elmid beetles was more variable inter-annually in pools and low gradient reaches than in high gradient reaches. Differences in the percentage of collector-gatherers and scrapers in riffles and pools appeared related to inter-annual differences in discharge regimes. Two components of the annual discharge regime appear to differentially affect the composition of the benthic community in the snowmelt dominated stream studied: the magnitude of the annual peak discharge and the duration and timing of the period of extended high flow.