We examined the associations of microorganism assemblages with a complete mineral richness gradient spanning from extremely mineral-rich tufa-forming calcareous fens to mineral-poor acidic Sphagnum-fens. We also compared the distribution of two dominant taxa, testate amoebae and monogonont rotifers, among the sites differing in water chemistry and among three microhabitats sampled at each site differing in substrate and moisture conditions. Microorganism assemblages primarily changed in relation to the mineral richness gradient; moisture was the second most important factor structuring microorganism assemblages among microhabitats (i.e., wet bryophytes, submerged bryophytes and waterlogged bottom sediments). Densities of testate amoebae taxa and individuals were the highest in rich Sphagnum-fens, indicating a unimodal pattern along the mineral richness gradient. Numbers of testate amoebae taxa decreased notably in wet bryophytes, especially in poor Sphagnum-fens. This pattern might result from a strong effect of Sphagnum acidification due to minimal or no dilution of the acidic environment by mineral-rich groundwater. As a consequence, acid tolerant and relatively xerophilous taxa chiefly dominated in wet bryophytes of poor Sphagnum-fens, while poor Sphagnum-fen bottom sediments could provide a refuge for less tolerant and hydrophilous species. In contrast to testate amoebae, monogonont rotifers preferred bryophytes in all sites, with the number of monogonont taxa distinctly increasing from calcareous fens to poor Sphagnum-fens. In poor Sphagnum-fens, monogononts were the most abundant in wet bryophytes, probably due to reduced food competition and/or predaceous pressure resulting from the limited occurrence of other groups of microorganisms by virtue of the hostile acidic conditions in wet Sphagnum carpets.