This paper presents results of the studies of ciliate assemblage in benthos of lowland river influenced by sewage discharged from the municipal wastewater treatment plant. During the presented research the 47 ciliate species, including 45 species from the benthos of the river and 18 from the activated sludge of aeration chamber were identified. Only two species registered in the activated sludge were not observed in the river. Against the background of the lowest number of species in the point located in the distance of 50 m below the discharge of sewage the maximum amount and biomass of these species were observed. Whereas, 200 m below the discharge the decrease in number and biomass of ciliate to the level noted for location before the discharge was observed. Thus, generalizing, one may state that influence of municipal WWTP sewage discharge for ciliate assemblage in the river’s benthos was clearly visible but local.