Freshwater diatoms are considered to be reliable indicators of the trophic status of rivers and lakes. In the past 30 years, a number of indicator indices have been developed and used for the assessment of trophic conditions all over Europe. It is however still not clear whether the ecologic signature of diatoms differs between these indicator indices. The present study assessed a large number of published European indices on the response of freshwater diatoms to trophic conditions by evaluating the consistency in the use of taxa and their trophic score from seven European indicator indices. The STAR (Standardisations of River Classifications) diatom database, a large set of samples from European running waters, was used to test the application of trophic classifications in water quality assessment. The analysis of taxa in common within the trophic indices showed that there are considerable differences between the indices, for example in the score of trophic values. There was more agreement in classification of taxa within the oligotrophic and the hypertrophic preferences than within the mesotrophic range. Based on these results, a list of diatom taxa, that are consistently used in different trophic indices, was composed. It included 159 ‘reliable’ taxa that are not sensitive to regional setting, water type and taxonomic uncertainty. The list was further accompanied by a description of the taxa's trophic preferences. The large deviation in trophic scores for a number of diatom taxa could most probably be explained by taxonomic uncertainties. Application of these taxa for trophic assessment was questionable. The test set of the 359 STAR samples showed that differences between the trophic indices also lead to a significant variation in the water quality assessment results. Although trophic indices provide an excellent biomonitoring tool, they should be applied with caution, considering the recommendations provided in this paper.