The sediments of two Eocene oil shale lakes (Messel Graben and Eckfeld Maar, West Germany) were analyzed with respect to the distribution, chemical and stable isotope composition of siderite. The data allow a reconstruction of different stages in the sedimentary and early diagenetic history of the lakes. In the Messel lake, siderite formation started when the sedimentation of laminated, sapropelic, C org-rich sediments was already established. The early stage of oil shale sedimentation was characterized by pyrite precipitation; in the siderite stage the stable isotope composition of the carbonate suggests methanogenesis to have been an important process at the sediment/water boundary layer. In the Eckfeld lake, siderite formation started even before sedimentation of the first sapropelic laminae. The stable isotopic composition of the carbonate again indicates an anoxic sediment/water boundary layer and strong methanogenesis. With the expansion of this environment into the deep water mass, sapropel sedimentation became established. For both sequences, the chemistry and stable isotope composition of the siderites correlates with petrographic and paleontological information about climate-dependent fluctuations in the ecological, chemical, and early diagenetic environment. The strong relationship of siderite formation to methanogenesis may be explained by the rate of microbial organic matter degradation, which governed both methanogenesis and P CO2.