Ciliate assemblages, together with phytoplankton and heterotrophic nanoflagellates (HNF) as their potential food, have been surveyed monthly along the salinity gradient of the Nervión River estuary from March 2000 to March 2002. A total of 135 taxa of ciliate have been identified corresponding to 20 orders. Scuticociliates, naked choreotrichs and oligotrichs were the most abundant groups, distributed throughout a broad range of salinity. In addition to these groups, which were the dominant taxa in the middle estuary, tintinnids were characteristic of the ciliate assemblages of the outer estuary whereas in the innermost part naked choreotrichs and oligotrichs decreased in number, being substituted by sessilids, hymenostomatids, peniculids and cyrtophorids. Total ciliate concentrations were among the highest reported in the literature for other estuaries and coastal waters, frequently reaching 10 5 cellsl −1 . Meanwhile, tintinnid concentrations were comparable with those of other estuarine and coastal waters. Based on a principal component analysis (PCA) three main groups were delineated, with ciliates and their potential food sources as variables. One was that constituted by freshwater ciliate such as sessilids, hymenostomatids, cyrtophorids and pleurostomatids, which appear in low numbers in the innermost part, mainly in winter. Another group contained diatoms, chlorophytes, flagellates, euplotids and scuticociliates, all of them broadly distributed along the estuary and reaching their maximum density in late spring–summer. The third group was made up of taxa mainly appearing at the seaward end such as dinoflagellates, cyanobacteria, haptorids, tintinnids, naked choreotrichs and oligotrichs, which reached the highest densities in summer and early autumn. Ciliates do not seem to be food limited in the Nervión River estuary or much controlled by metazoan grazing.