The aim of this study was to examine relations between the density and species richness of ciliates and rotifers in 6 peatlands (2 raised bogs, 2 poor fens, 1 typical fen, and 1 base-rich fen), in Polesie National Park in southeastern Poland. Their relations with selected chemical parameters were also analyzed. The peatlands differed in pH, conductivity, total phosphorus, nitrates, and total organic carbon concentrations. The study showed that the microbial communities are most strongly dependent on concentrations of total organic carbon, nitrates, phosphates, and total phosphorus. It seems that nutrients and total organic carbon have an indirect influence on the abundance of ciliates and rotifers, through the control of food abundance (mainly bacteria). Additionally, ciliates are most abundant in spring and autumn, when rotifers are infrequent. This suggests that rotifers, as competitors, could be the main regulators of ciliate abundance in surface water of peatlands.