Methanogenesis, an anaerobic microbial process in sediments, was investigated in a naturally acidic bog lake, Grosse Fuchskuhle, in northeastern Germany. The lake was artificially divided into four sub-basins: two western basins receiving humic substances from an adjacent Sphagnum bog and two eastern basins isolated from this acidic inflow with installed curtains. Within the northeast (NE) and southwest (SW) basin compartments, one of each group were studied. In the peat influenced western basins the pH-values in the water columns were kept low and increased in the others. The stratification period increased in all four compartments from some weeks to some months, from April to October, with the development of anoxic hypolimnia in all compartments after the installation of the curtains. The layer with the most active methane production moved from a sediment depth of more than 20 cm before separation to close to the surface sediments in all compartments. Methano genic microorganisms were found in the whole sediment core – from surface sediments to a depth of 25 cm. The proportion of methanogens was approximately 15% of total microbial cell numbers, which were approximately 2 × 106 cells/ml sediment. Oligonucleotide probes targeting nearly all families of the phylum Euryarchaeota were tested with fluorescence in-situ hybridization (FISH). In both basins, with and without the influence from peat, oligonucleotide probe (MSMX) targeting Methanosarcinaceae could be detected only as methanogens. The finding of only acetate-using methanogens by FISH indicated acetate as a major methanogenic substrate. Concentration profiles of CH4 as a function of sediment depth were characterized in both basins by high concentrations in the top layers. Methane bubbles were released in the late summer in the eastern sub-basin only, likely from oversaturation in the surface sediments.