The primary objective of the present study was to determine the seasonal dynamics of ciliates in activated sludge. Studies were carried out in order to verify the hypothesis that fertility of a habitat may significantly influence the seasonal dynamics of the abundance of ciliates, as well as the number and intensity of correlations between physic-chemical parameters and ciliates. It seems that the values of numbers of ciliates were seasonally changeable. The highest numbers of ciliates were found in spring and summer, however the lowest numbers of ciliate communities were noted in winter. The studies showed that protozoa community is determined by ammonia mainly in summer. In spring and winter additional factors may be important. Probably suspended solid, total organic carbon and concentration of appropriate food (bacteria and flagellates) are the major regulator of abundance of ciliates.