The UK River Habitat Survey (RHS) method for the assessment of hydro-morphological features was applied within the EU STAR project simultaneously with the collection of biological data. A subset of data from 79 sites affected by hydro-morphological alteration and belonging to 7 different stream types was analysed. The different features recorded within RHS were evaluated separately considering the characteristics associated with banks, channel and riparian zone. Different scores were assigned to selected features representing hydro-morphological alteration and naturalness of habitat. The ability of the different compartments to represent the quality gradient of sites was investigated. In addition, the link between macroinvertebrate community and hydro-morphological data was investigated, directly relating indices and metrics calculated from taxa list collected in a site to scores assigned to the RHS features. The sections highly affected by morphological alteration were channel geometry and bank profile. Metrics showing the best correlation with the features selected were EPT taxa, ASPT and ICMi (Inter-calibration Common Metric index). Among the indices studied, the HQA score (Habitat Quality Assessment) apparently played the most important role in structuring biological communities and the lentic-lotic character of rivers was also important.