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Biomarkers of aquatic algae and compound-specific carbon isotopes are used to examine past variations in algal community composition and primary productivity in Lake Malawi. We note major changes at the Pleistocene-Holocene boundary. From the Last Glacial Maximum until ∼11.8 calendar years before present (kyr B.P.), Lake Malawi was characterized by either low rates of primary productivity or algal productivity that was dominated by a group other than diatoms. At the onset of the Holocene, conditions similar to those of modern Lake Malawi were initiated, with diatoms and nitrogen-fixing cyanobacteria becoming more important contributors to primary productivity. The transition at ∼11.8 kyr B.P. is likely related to a shift in the dominant wind direction over Lake Malawi, resulting from a southward shift in the mean latitudinal position of the Intertropical Convergence Zone during the last glacial. Throughout the 23-kyr B.P. record, the effects of wind-induced upwelling are important and may be the main control on the carbon isotopic composition of algal lipids through delivery of 13C-depleted CO2, derived from organic matter decomposition in deeper waters, to the photic zone. Relationships are also suggested between thermal stratification and primary productivity, with cool conditions at ∼12 and 8 kyr B.P. resulting in weaker thermal stratification and increased primary productivity. The opposite situation occurs at 4.9 kyr B.P., when significantly warmer temperatures and decreased algal productivity are observed. Thus, in lentic systems such as Lake Malawi the major influence of climate on algal ecology appears to be through feedbacks in physical circulation mechanisms. [ABSTRACT FROM AUTHOR]