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Wetlands restoration has been implemented on sites exploited for agricultural for over a decade in Eastern Europe. However, little is known about microbial diversity in this region. Microbial processes and patterns can be used as sensitive indicators of changes in environmental conditions. The responses of ciliates wetlands restoration are largely unexplored. Based on the results of a long-term study in fen of the Poleski National Park (Poland), we assumed that restoration causes changes in the physicochemical properties of fen water and sought to answer the question of how ciliate communities react to these changes and whether these microorganisms can play a significant role as bioindicators in evaluating the restoration process. Twenty taxa were recorded in the ciliate community, with 16 taxa found prior to restoration and 12 after restoration. Restoration clearly modified the taxonomic composition and abundance of ciliates. This was reflected in a decrease in the abundance and in the density of these protozoa and in a significant increase in the proportion of euplanktonic species. Before restoration, the most common ciliates were Cinetochilum margaritaceum and Strombidium viride, while the proportion of Paramecium bursaria increased after restoration. We also observed that the improvement in hydrological conditions, and hence the transformation of the vegetation structure in the peat bog, causes changes in the trophic structure of ciliates. The RDA analysis showed that all variables together accounted for 86.9% of the total variance. However, variables that significantly explained the variance in ciliate communities were water level, temperature, pH, and nutrients. Our results suggest that an indicator species approach based on functional groups may be appropriate for biomonitoring fens restoration.