Several methods for water quality assessment have been proposed for European rivers. The EU Water Framework Directive requires the use of ecological indicators for stream monitoring networks and has encouraged research on biological indices. However, there is a lack of integrative studies comparing the efficiency of such methods in the determination of the ecological status in rivers. The present work, carried out in the Spanish side of the Duero Basin, the largest in the Iberian Peninsula, aimed at comparing different water quality indices. The survey was conducted during autumn 2003 and summer 2004 in 95 sites covering the entire basin. Epilithic diatoms and benthic macroinvertebrates were sampled and analysed following standard methods for the calculation of the macroinvertebrate index IBMWP and 18 different diatom indices. Additionally, water physical and chemical variables were measured and Habitat (IHF) and Riparian (RQI) indices were determined in situ. In general, both diatom and macroinvertebrate indices were strongly correlated with each other and with abiotic factors. The highest correlation coefficients between water physical and chemical data (especially with the concentrations of phosphates and N-derived compounds) were obtained for the diatom index SPI and the IBMWP, though no biotic method detected changes in the concentrations of toxicants (Zn 2+ , Cr III). The use of diversity metrics as monitoring indices is not recommended. The results indicated that several different biotic indices, based on a wide range of biotic communities, must be integrated in water quality surveillance protocols, in order to reflect complementary aspects of the ecological status in river ecosystems.