Abstract. Temporal drying of upper soil layers of acidic methanogenic peatlands might divert the flow of reductants from CH4 formation to other electron-accepting processes due to a renewal of alternative electron acceptors. In this study, we evaluated the in situ relevance of Fe(III)-reducing microbial activities in peatlands of a forested catchment that differed in their hydrology. Intermittent seeps reduced sequentially nitrate, Fe(III), and sulfate during periods of water saturation. Due to the acidic soil conditions, released Fe(II) was transported with the groundwater flow and accumulated as Fe(III) in upper soil layers of a lowland fen apparently due to oxidation. Microbial Fe(III) reduction in the upper soil layer accounted for 26.7 and 71.6% of the anaerobic organic carbon mineralization in the intermittent seep and the lowland fen, respectively. In an upland fen not receiving exogenous Fe, Fe(III) reduction contributed only to 6.7%. Fe(II) and acetate accumulated in deeper porewater of the lowland fen with maximum concentrations of 7 and 3 mM, respectively. Both supplemental glucose and acetate stimulated the reduction of Fe(III) indicating that fermentative, incomplete, and complete oxidizers were involved in Fe(II) formation in the acidic fen. Amplification of DNA yielded PCR products specific for Acidiphilium-, Geobacter-, and Geothrix-, but not for Shewanella- or Anaeroromyxobacter-related sequences. Porewater biogeochemistry observed during a 3-year-period suggests that increased drought periods and subsequent intensive rainfalls due to global climate change will further favor Fe(III) and sulfate as alternative electron acceptors due to the storage and enhanced re-oxidation of their reduced compounds in the soil.