Chironomid larvae and pupae were studied in selected Mediterranean rivers with the aim of identifying pool and riffle taxa assemblages and of analysing their response to ecological quality gradients. Macroinvertebrate samples were collected in six Italian rivers along a pool-riffle sequence in three seasons following a multihabitat sampling technique. Chironomids were identified as genus/species, other macroinvertebrates as family/genus. The main physico-chemical, hydromorphological and geographical data were collected. Samples were ascribed to five quality classes according to the STAR_ICM index. Based on Chironomid taxa, principal component analysis (PCA) axis 1 represented an organic pollution gradient, axis 2 represented seasonality. Pool and riffle samples were significantly different according to taxa assemblages. Similar results were obtained with PCA based on the whole macrobenthic community. Indicator value (IndVal) analysis facilitated the detection of the Chironomid indicators of high/good quality pools (e.g. Conchapelopia pallidula, Rheopelopia ornata, Epoicocladius ephemerae) and riffles (Tvetenia calvescens, Eukiefferiella gracei). The Berger–Parker dominance index based on Chironomid assemblages in pools was correlated to PCA axis 1 and performed well in discriminating between quality classes. In riffles, no correlations to PCA axes were detected and a wide overlap between quality classes was present. Thus, assessment in the analysed river type may focus on pool mesohabitat as this seems to represent best the ecological gradient of sites. Copyright © 2009 John Wiley & Sons, Ltd.