A Pliocene-age volcano on Penguin Island became active again in the Pleistocene/Holocene, forming the main cone of the island – Deacon Peak, and leaving late-Holocene phreatomagmatic craters, including ‘Petrel Crater’, about 200 m in diameter and filled currently by a maar lake with a flat bottom at 18 m water depth. Petrographic, geochemical, photosynthetic pigment, and diatom data from the 72-cm-long sediment core reveal that the crater was initially a marine lagoon with typical phytoplankton assemblages. Most probably, tectonic–volcanic activity about 1250 years ago, documented in tephra fallout, triggered an abrupt glacio-isostatic uplift that separated the lake from the sea. The horizon of tephra, probably from the Deception Island volcano, marks a sudden change in environment from brackish to lacustrine. The ecological evolution of the lake was initially constrained by an uplift, whereas the influence of marine water vanished with time, the lake became meromictic, and the freshwater mixolimnion layer expanded, while the monimolimnion became anoxic due to the influence of a penguin rookery situated on the shore. During the ‘Little Ice Age’ (LIA), the maar may have been covered by permanent ice. A discharge of mineralized guano from the possibly enlarged penguin rookery on the lake shore caused an expansion of the anoxic monimolimnion to the ice surface and an important reduction of autochthonous lacustrine biota of the maar, whereas a substantially increased participation of allochthonous biota passively supplied with guano. That record in the lake sediment core reaffirms the occurrence of a regional LIA event in the maritime Antarctic.