1. Over the last decade the development of small hydropower projects has been one of the most active areas of the energy sector. One of the main environmental challenges faced by such projects is related to fish passage. 2. The impact of 18 small hydropower plants (SHPs) with distinct levels of fish-pass effectiveness was investigated in the summers of 1998 and 1999 by comparing fish assemblage composition and structure at 36 sites, above and below SHPs. 3. With regard to effectiveness, it was estimated that eight (44.4%) of the surveyed passage facilities were suitable for target species, whereas the remaining 10 (55.6%) were considered unsuitable. In neither case did the composition of fish assemblages upstream and downstream from SHPs differ significantly, while assemblage similarity was relatively high. 4. Multivariate techniques identified cover, depth and coarse substrate as the main parameters structuring fish assemblages. It is suggested that these variables have created a rich, patchy, heterogeneous habitat, thereby providing satisfactory resources and favourable conditions required by fish and contributing to the maintenance of assemblages. 5. Although populations of some species that occurred both upstream and downstream from SHPs have developed differences in their size structures, SHP-induced fragmentation of fish populations may not necessarily result in genetic divergence among semi-isolated populations. Copyright © 2006 John Wiley & Sons, Ltd.