Fossil pigments were identified in a sediment core from Kirisjes Pond, a small lake in the Larsemann Hills, east Antarctica, using reversed-phase HPLC and LC–MS/MS. Chlorophyll a- and b-derived components indicate the presence of oxygenic primary producers; steryl chlorin esters provide evidence of grazing, while shifts in their esterifying sterol composition record changes in the primary producer community. Bacteriochlorophyll c- and d-derived components, indicative of photic zone anoxia, were identified with structural variations including extensive alkylation in the macrocycle up to C6. The pigment distribution reveals a change from oxygenated freshwater to a stratified water body with development of photic zone anoxia. This coincides with a marine incursion identified from diatom records and is followed by re-isolation and reversion to oxygenated freshwater conditions