Peatlands are extremely valuable ecosystems of enormous biological diversity, mainly due to their specific geological and hydrological conditions. One of the most important threats facing these habitats is overgrowth resulting from intensifying succession processes. Due to the fact that peatlands are endangered or vanishing, attempts are made to restore their original natural assets. The aim of the present study was to determine the effect of active conservation of peatland ecosystems, in the form of removal of birch trees, on communities of ciliates. The subject of the research was the Durne Bagno peat bog, located in Polesie National Park in eastern Poland. Analysis of the results of long-term research (nine years) showed that active conservation measures affect the physical, chemical, and hydrological properties of peatlands. In the habitat where birch trees were cut down, the water level, temperature, and chlorophyll a concentration in the vast majority of cases were higher than in the area with Betula L. Changes in habitat conditions are reflected in the taxonomic composition and abundance of ciliates. In the habitat from which birch trees were removed, ciliate abundance was higher than in areas where birch remained. The total number of taxa in the habitats was the same, but there were seasonal differences. The most taxa were recorded in spring and summer and the fewest in autumn. Thus, analysis of the results indicates that ciliates are an appropriate indicator group of species for biomonitoring of peatland restoration.