The most remote regions of the globe are home of the least disturbed ecosystems, yet they are threatened by air pollution and by climatic change. The Himalayas are one of the most isolated and least explored wilderness areas in the world outside the Polar Regions and it is for this reason that the Tibetan Plateau is often referred to as the ‘Third Pole’. Since 1990, an annual limnological survey (including chemistry and biology) has been carried out at two lakes located in the Kumbhu Valley, Nepal, at 5200 and 5400 m a.s.l., respectively. Lake water chemistry surveys reveal a persistent increase in the ionic content of the lake water, a trend which appears to be closely linked to increasing temperature. In this study, we also analysed lake sediment cores for historical changes in algal abundance and community composition to evaluate how long-term variations in primary producer communities corresponded to known regional variations in climate systems during the past 3500 years. Paleolimnological results support the evidence that the strong variability observed in the chemical data drives the variability in lake production and in the composition of algal assemblages. These variabilities can be related to known features of local climate and the values recorded in the recent years compare well with those recorded during warm periods, such as around 2000 BP, and thus support the idea that this area of the Himalayan Range, influenced by the South Asia monsoon, is closely linked to Northern Hemisphere climate dynamics.