Lake sediments are key archives for paleoenvironmental investigation as they provide continuous records of the depositional history of the lake and its watershed. Lake Futalaufquen (42.8°S) is an oligotrophic waterbody located in Los Alerces National Park in the Andes of northern Patagonia, South America. A sedimentary sequence covering 1600 years was recovered to analyze the potential for paleoenvironmental reconstructions of the last millennia. Integration of different geochemical and mineralogical parameters and comparison with climatic reconstructions from other Patagonian records give clues for the identification of a warm period around AD 800–1000, associated with the Medieval Climatic Anomaly. The high frequency of tephra layers beginning in the mid-sixteenth century precludes identification of the Little Ice Age, recorded in northern Patagonia as a cold period from the fourteenth to the eighteenth century. Furthermore, the parameters analysed do not provide evidence of late-twentieth-century global warming. However, Zn deposition, a long-distance atmospheric transport process of anthropogenic origin, was identified during the last century.