The sediments that now comprise the Messel shale¹ accumulated 47 ± 2 million years ago in anaerobic waters at the bottom of a lake². Subsequent depths of burial have not exceeded 300 m, nor has the temperature of the shale exceeded 40 ^°C³. Contents of organic carbon reach 25%, and preservation of molecular structures has been excellent^4,5. Sixteen different geoporphyrins, including three derived from bacteriochlorophyHs of the d series and thus indicative of the existence in the lake of an anaerobic photic zone, have been isolated and identified^6–8. Here, we show that the carbon isotopic compositions of these and other biomarkers allow identification of specific sources for some materials and reconstruction of carbon flows within the lake and its sediments. The ¹³C content of organic matter synthesized by lacustrine primary producers can be estimated from the observed ¹³C content of the geoporphyrins derived from their chlorophylls. Total organic material in the shale is depleted in ¹³C by six parts per thousand relative to that input. This difference cannot be explained by selective loss of components enriched in ¹³C, nor, as shown by isotopic compositions of other biomarkers, by inputs from land plants surrounding the lake or from methanogenic bacteria.