Comparing the organic matter (OM) composition of modern and past lake sediments contributes to the understanding of changes in lacustrine environments over time. We investigate modern plant and lake-water samples as well as modern and ancient sediment samples from the Tswaing Crater in South Africa using biomarker and stable carbon isotope analyses on bulk OM and specific biomarker compounds. The characteristic molecular markers for higher land plants (predominantly C3-type deciduous angiosperms) in Lake Tswaing are long-chain n -alkanes ( n -C27−33), n -alkanols ( n -C28+30), stigmasterol, β-sitosterol, β-amyrin, α-amyrin and lupeol. The C17 n -alkane, tetrahymanol, gammaceran-3-one and C29 sterols dominate the lipid fraction of autochthonously produced OM. By comparing stable carbon isotope analyses on bulk OM and the characteristic biomarkers, we follow the modern carbon cycle in the crater environment and find indications for methanotrophic activity in the lake from isotopically depleted moretene. A comparative study of core sediments reveals changes in the terrestrial (C3 versus C4) and aquatic bioproductivity and allows insights into the variability of the carbon cycle under the influence of changing climatic conditions for the time from the end of the last glacial (Termination I) to the late Holocene, ca. 14,000–2,000 calibrated years before present (years BP). The most pronounced changes occur in the aquatic realm after ca. 10,000 years BP when our results imply climate swings from more humid to more arid and after 7,500 years BP to gradually more humid conditions again, which can be related to a shift in the position of the Inter-Tropical Convergence Zone or to changes in the tropical atmosphere–ocean interaction. Long-chain alkenones (LCAs) have been identified in ancient lake sediments from Africa for the first time. They occur in samples older than 7,500 years BP and their distribution (dominance of C38 and of tri- over tetra-unsaturated LCAs) is distinctly different from other published records suggesting a to date unknown source organism. ©2009 Springer Science+Business Media B.V.