Two long-term submerged Eutric Gleysols (GLe) and two short-term flooded Eutric Fluvisols (FLe) with high organic carbon contents (C_org between 5.1 and 12.9%) were selected to characterize soil microbial communities at the Elbe River (Germany). Measurements included dehydrogenase activity (DHA), soil microbial carbon (C_mic), soil basal respiration (BR), metabolic quotient (qCO₂), C_mic/C_org ratio, and phospholipid fatty acids (PLFA). PLFA biomass, DHA, and C_mic/C_org ratios were considerable lower in GLe's than in FLe's. Whereas the BR as well as qCO₂ were higher in GLe's what seems to be an unspecific response of aerobic soil microorganisms to the long flooding period and the resulting short time for development following flooding. C_mic/C_org ratios were low in comparison to terrestrial soils. PLFA profiles were dominated by saturated fatty acids (FA). Principal component analyses (PCA) of FAs revealed clear differences among the four floodplain soils. In GLe's all fractions of PLFAs were lower than in FLe's. Polyunsaturated FA biomarkers (18:2ω6,9c) were 10 times lower in GLe's. Our results indicate that the environmental conditions in which microorganisms are exposed (i.e., long term soil inundation and anoxia) seem to be disadvantageous for fungi.