Biological invasion and environmental change pose major threats to ecosystems. While long-term ecological change is commonly evaluated through sediment cores in lakes, it is generally not feasible for smaller ponds, and spatial resolution is limited. Here, we analyze pond diatom communities collected during Shackleton's Nimrod expedition at Cape Royds, Antarctica, to compare with the same waterbodies a century later. We find historical samples to be almost identical to modern counterparts, and provide no evidence of exotic introductions despite increasing human activity. However, a shift occurred in the pond nearest Shackleton's hut, Pony Lake, which was dominated by Luticola muticopsis a century ago, and was replaced by Craspedostauros laevissimus. Both are endemic species previously and currently present at Cape Royds, and we hypothesize that a shift in conductivity accompanying changing precipitation patterns may be responsible. Collectively, these results provide important data for assessing human and climate impacts among Antarctic lacustrine habitats.