The aim of this study was to examine the community structure and vertical micro-distribution of testate amoebae and ciliates in a raised bog in eastern Poland, as well as to assess the influence of potential food resources (Chl-a, bacteria, heterotrophic flagellates) and predators (rotifers and copepods) on protozoa communities. Samples were taken from surface, bottom and interstitial waters. At each type of micro-habitat and each sampling date water was sampled using a plexiglass corer or mini-piezometers. Additionally, in order to evaluate grazing pressure, field enclosures were used in which metazoan abundance and composition was manipulated by size-fractionation. Over experiments, metazoan populations shifted from dominance of rotifers to copepods. In the first experiment, with rotifers dominating, metazoa had only a modest predatory impact on the protozoa. In contrast, the second experiment, with copepods prevailing, demonstrated a clear top-down control of the protozoa communities by metazoan. The density and biomass of protozoa significantly differed between the studied stations, with the lowest numbers in the interstitial water and the highest in the surface water. Surface sampling were dominated by mixotrophic taxa, whereas the deepest sampling level was characterized by increase in the proportion of bacterivore species. These differences between micro-habitats may be due to differences in environmental conditions (food resources and grazing pressure). Ordination analysis revealed that bacteria can strongly regulate the abundance and taxonomic composition of protozoa in the bottom and interstitial waters. Metazoan predators could be the main regulators of protozoa communities in surface water.