Summary Ciliated protozoa were collected from six stations during one year from water-sediment interface of a branch located in the hill zone of the River Stirone and its polluted tributary Torrente Ghiara. Three stations were located upstream the confluence of T. Ghiara, two stations were located downstream, and one was located at T. Ghiara before the confluence with the River Stirone. A total of 147 species of ciliates belonging to 90 genera were found. Their distribution and abundance varied greatly both along the river and with time. Community structures were analysed using some statistical methods and this allowed the determination of similarities among stations and between species and stations. The saprobic index and valency methods were used together with specific diversity analysis to quantify organic input and to follow their change in time. A marked change in the ciliate community was observed between stations located upstream and stations located downstream being influenced by polluted water from Ghiara stream. The former were composed of β-mesosaprobic species, typical of the hill zone of running waters, while the latter were composed of α-mesosaprobic and polysaprobic species typical of various-typologies stations but all characterized by organic pollution. Our results suggest that in watercourses the organic load may be the dominating factor able to influence, if not eliminating, the diversifying effects of other factors such as those which characterize the longitudinal zonations of the watercourses.