Palaeoclimate changes, such as the Medieval Climate Anomaly and the Little Ice Age, are well-defined in the Northern Hemisphere during the past 2000 years. In contrast, these anomalies appear to be either absent, or less well-defined, in high-latitude regions of the Southern Hemisphere. Here, we inferred environmental changes during the past two millennia from proxies in a sediment core from Mago Ike, an East Antarctic lake in Skarvsnes (Lützow Holm Bay). Variations in lake primary production were inferred from fossil pigments, sedimentological and geochemical proxies and combined with absolute diatom counts to infer past diatom productivity and community changes. Three distinct stratigraphic zones were recognized, resulting from a shift from marine to lacustrine conditions with a clear transition zone in between. The presence of open-water marine diatoms indicates a coastal zone seasonally free of sea ice between c. 2120–1500 cal yr bp. Subsequently, the lake became isolated from the ocean due to isostatic uplift. Freshwater conditions were established from c. 1120 cal yr bp onwards after which the proxies are considered highly sensitive to temperature changes. There is no evidence for a Medieval Climate Anomaly, Little Ice Age or twentieth century warming in our lake sediment record suggesting that studies that have imposed Northern Hemisphere climate anomalies onto Southern Hemisphere palaeoclimate records should be treated with caution.