Samples were collected monthly from the water-sediment interface at six stations along the Mincio River (northern Italy) during a 1-year study of the ciliated protozoan communities. Four stations were located upstream of the Mantua lakes in the hyporhithron fluvial zone and two stations were located in the potamon fluvial zone between the Mantua lakes and the confluence with the Po River. A total of 133 species of active trophic ciliates belonging to 76 genera were found. Community structures revealed in this data were analysed using some statistical methods (similarity index, and categorical principal component analysis (CATPCA)) and this allowed the determination of differences between stations and between ciliate communities characteristic of stations. Species typical of the ecotypes located in both rhithron and potamon fluvial zones were defined. The saprobic index and valency analysis methods were used to quantify organic input and to follow changes in saprobicity along the river. A change in the ciliate communities was observed between stations located upstream and stations located downstream of the town of Mantua. The former were composed mainly of beta-mesosaprobic species, typical of the hill zone of running waters, while in the latter increased numbers of alpha-mesosaprobic species are associated with the higher anthropogenic pressures. Our results reiterate the high sensitivity shown by ciliated protozoa as indicators of organic load in watercourses.