Recent research into the physical and ecological status of rivers has focused upon rapid field-based assessments of mesoscale habitat features in order to satisfy international regulatory requirements for habitat inventory and appraisal. Despite the low cost and time efficient nature of rapid field surveys, the robustness of such techniques remains uncertain. This paper uses data from over 4,000 surveyed UK river reaches in the UK River Habitat Survey (RHS) database in order to seek linkages between surface flow conditions (flow biotopes), local channel morphology (physical biotopes) and biologically distinct vegetative and minerogenic habitat units (functional habitats). Attempts to identify one-to-one connections between surface flow types, units of channel morphology and functional habitats oversimplify a complex and dynamic hydraulic environment. Instead, a nested hierarchy of reach-scale physical and ecological habitat structures exists, characterised by transferable assemblages of habitat units. Five flow biotopes show strong correlations with functional habitats, and differing combinations of three of these account for over 60% of the distribution for all functional habitats. On this basis, a classification of environments for ecological purposes is proposed. Principal components analysis and agglomerative hierarchical clustering analysis are employed to objectively validate the proposed classification. Flow biotope assemblages may also represent reach-scale channel morphologies (step-pool, riffle-pool and glide-pool), although functional habitats exhibit differing 'preferences' for rougher or more tranquil environments within these. While the data and analysis are specific to the UK RHS, the methods and findings have wider application in situations, where rapid field appraisal methods and associated databases are deployed in water resource inventory and river rehabilitation design.