We analysed the response of microbial communities, characterized by phospholipid fatty acids (PLFAs), to changing hydrological conditions at sites with different nutrient levels in a southern boreal peatland. Although PLFAs of Gram-negative bacteria were characteristic of the peatland complex, microbial communities differed among sites (ombrotrophic bog, oligotrophic fen, mesotrophic fen) and sampling depths (0–5, 5–10, 10–20, 20–30 cm). The microbial communities in each site changed significantly following water-level drawdown. The patterns of change varied among sites and sampling depths. The relative proportion of Gram-negative bacteria decreased in the upper 10 cm but increased in deeper layers of the fen sites. Fungi benefited from water-level drawdown in the upper 5 cm of the mesotrophic fen, but suffered in the drier surfaces of the ombrotrophic bog, especially in the 5–10 cm layer. In contrast, actinobacteria suffered from water-level drawdown in the mesotrophic fen, but benefited in the drier surfaces of the ombrotrophic bog. Basal respiration rate correlated positively with pH and fungal PLFA, and negatively with depth. We suggest that the changes in microbial community structure after persistent water-level drawdown follow not only the hydrological conditions but also the patterns of vegetation change. Our results imply that changes in structure and activity of the microbial community in response to climate change will be strongly dependent on the type of peatland.