Determining the influence of physical habitat on biological structure in minimally disturbed settings is important if the effects of alterations to physical habitat are to be understood. This study tested whether reach-scale differences in physical habitat influence macroinvertebrate community composition at 24 sites in the Cairngorm Mountains, Scotland. Stream reaches were classified into channel types based on a geomorphic typology (i.e. step-pool, bedrock, plane-bed and pool-riffle). PERMANOVA indicated an overall significant relationship between the geomorphic typology and macroinvertebrate species-level composition, and among all combinations of channel types (such as step-pool and pool-riffle, step-pool and bedrock). Most channel types were dominated by high abundances of Baetis rhodani, Rhithrogena semicolorata and Leuctra inermis, which are ubiquitous in unpolluted gravel-bedded Scottish streams. However, reflecting significant differences in abundance of commoner taxa between types, indicator value (IndVal) analysis revealed that pool-riffle reaches were characterised by elmids (Limnius sp. and Oulimnius sp.) and Caenis rivulorum, and step-pool reaches by Alainites muticus, B. rhodani, L. inermis and Brachyptera risi. Geomorphic typing of rivers provides a useful basis for the initial assessment of ecological status whereas abundance-based biological data processed at the appropriate taxonomic resolution should be sensitive to physical-habitat modifications.