We characterized channel unit types in 13 steep, headwater streams in British Columbia, Canada, based on physical variables, to determine the influence of channel unit type on benthic macroinvertebrate assemblages. Macroinvertebrate abundance was highest in riffles, followed by rapids, pools, boulder cascades, chutes, and bedrock cascades. Heptageniidae, Nemouridae, Chironomidae, Leptophlebiidae, Enchytraeidae, Chloroperlidae, Lepidostomatidae, and Tricladida were most abundant in either riffles or rapids. Baetidae and Simuliidae preferred bedrock cascades and chutes, and predominance of these families resulted in a distinct assemblage structure within these 2 channel unit types compared with other types. Benthic assemblages within riffles, rapids, pools, and boulder cascades were not distinctive from each other. Significant interstream variation was apparent in abundance of all taxonomic groups studied. In general, invertebrates were more abundant in streams with perennial flow regimes compared to those with intermittent or ephemeral flow. Assemblage structure within ephemeral streams was distinct because of the preponderance of Enchytraeidae. Defining physical characteristics of stream channel units using benthic macroinvertebrate assemblages is a useful means of discriminating habitat conditions within small, high-gradient streams.