Traditionally, the interactions between geomorphic character and aquatic biodiversity have been widely acknowledged, but poorly quantified. However, the coupling of these disciplines is currently rising up legislative and political agendas, such as the European Union Water Framework Directive (EU WFD). The Directive requires Member States to classify rivers into types based on their natural morphology and geomorphic processes, and to link the biota to river types existing under natural conditions. Typing now forms the basis for evaluating environmental sensitivity to river engineering and determining reference conditions for river restoration. The Scottish Environment Protection Agency (SEPA) has adapted the Montgomery and Buffington (1997) channel typology developed in the Pacific Northwest of the USA for use in Scotland. The modified typology identifies eleven distinct channel types (e.g. bedrock, plane-bed, wandering and meandering). In this study, 43 reference condition sites in the upper River Dee catchment in the Cairngorms, Scotland were chosen to determine the geomorphic validity of the proposed typology, and assess whether channel types support a distinct macroinvertebrate community. Agglomerative Hierarchical Cluster Analysis failed to clearly identify eleven channel types based on catchment controls or on physical habitat characteristics. Four clusters were observed based on catchment drivers and six on physical habitat. Boundaries appear to be fuzzy, relating to a collective number of interacting environmental variables, geological discontinuities, and the geographic complexity of a river system. Multivariate ordinations and Analysis of Similarity indicated that macroinvertebrate communities only differed significantly between bedrock and step-pool reaches. A redundancy analysis showed differences in macroinvertebrate abundances among channel types were related to hydraulic, catchment drivers, physical habitat and physico-chemical variables. The results of the study have important implications for the use of geomorphic typologies in predicting aquatic biota.