Analysis of the predator-prey relationships is essential for understanding the functioning of peat pools. We investigated a set of peat pools – remnants of former peat extraction – and examined the impact of the common thecamoeba Arcella vulgaris on the major components of the microbial loop (algae, bacteria, heterotrophic flagellates and ciliates). The experiment consisted of two treatments under laboratory conditions, i.e. control versus the removal of Arcella vulgaris. The results suggest a substantial impact of Arcella vulgaris on the microbial communities, which is reflected in a decrease in abundance, biomass and a transformation of the size structure of bacteria towards smaller forms. Moreover, flagellate number and composition of algae were affected by this species. In both spring and summer, numbers of heterotrophic flagellates were significantly higher in the control than in the removal treatment. In spring, diatoms were dominant in the control, but their biomass decreased towards the end of the experiment, whereas in the removal treatment, a slight biomass increase of diatoms was observed. In summer, the biomass of cyanobacteria increased while that of desmids decreased in the control.