Leaf and rhizome litter was anaerobically decomposed in the soil substrates of three NE_German wetlands. The decomposition time was 75 days. Leaf litter from all sites was decomposed in all substrates, rhizome litter only in its home substrate. The decomposition experiment was done in the laboratory at room temperature by placing litterbags at the bottom of polyethylene containers (80 x 60 x 43 cm) filled with the specific soil substrates. The dataset contains litter CN-data, determined with an elemental analyzer, mass loss data, determined gravimetrically, data on the peak intensity of the proteinaceous bands Amide I and Amide II, determined via peak fitting of the vector normalized FTIR spectra (Origin Peak Analyzer), the increase of the asymmetric phosphodiester band due to litter decomposition, determined as the peak height of the second derivative difference spectra at 1220 cm-1, as well as, lignin phenol concentrations, determined by gas chromatography mass spectrometry after alkaline CuO oxidation of litter and soil substrates.