During the years 2008–2010 ciliated protozoa (Ciliophora) communities were monitored in hypertrophic shallow water reservoir. Continuously, 87 taxa of ciliates were found in pelagic environment and benthos. 7 of them were noted in Slovakia first time ( Actinobolina weinrichii, Balantidion pellucidum, Discophrya crassipes, Epistylis chrysemydis, Limnostrombidium pelagicum, Pelagohalteria cirrifera, Pseudostrombidium planctonicum ). On the basis of ciliated protozoa community analysis a negative impact of cyanobacteria and algae mass development was ascertained on its structure. Deteriorated effect appeared in the conspicuous instability of community during the year. Early spring-time (March) was characterized by the high diversity of ciliated protozoa with consecutive sharp decline (April) attended along with distinctive abundance growth as well as in plankton (late spring-time, early summer-time) after the massive formation of water-bloom. The high dominance of some species was recorded (especially Coleps hirtus, Paramecium caudatum, Cinetochilum margaritaceum, Frontonia leucas, Holophrya teres, Dexiotricha tranquila – selectively in particular months). A high portion of Suctorians and epizoic /colony-producing Peritrichichs were registered too. Feed spectrum alteration of some species ( Frontonia leucas, Coleps hirtus, Halteria grandinella ) was noticed.