The main objective of the Water Framework Directive (WFD) is to achieve good ecological status for surface waters in Europe by 2015. The ecological status has to be defined based on near-natural reference conditions. Benthic invertebrates and diatoms are among the key biological elements recommended by the Directive to assess ecological quality of water bodies. The purpose of this study is to identify species associations of these biological elements that are characteristic of the different stream types occurring in Luxembourg and that distinguish degraded from reference conditions. In general, the results reveal that diatoms and invertebrates can be considered as complementary indicators with more diatom species being characteristic of small size stream types and more benthic invertebrate species being associated with larger stream types. Among invertebrates, Trichoptera, Hydrachnidia, Ephemeroptera and Diptera show high affinities for most stream types. Plecoptera, Oligochaeta appear as useful indicators for some particular types. If only reference sites are selected (all river types considered), the number of indicator species drops from 55 to 24 for diatoms and from 81 to 48 for benthic invertebrates. Moreover, for the larger stream type, no reference site was found at all. This trend is likely to be a consequence of the multiple anthropogenic pressures that have affected large parts of European lowland rivers for decades. Our results suggest that Trichoptera, Hydrachnidia, Diptera, Ephemeroptera and Oligochaeta could be considered as best candidate groups for a tiered-taxonomic resolution approach where only taxa which have narrow and specific ecological requirements would be identified to finer levels. In Central Europe, however, since taxonomic soundness and easy recognition are required, only Trichoptera and Ephemeroptera are the groups to be recommended at the present time.