Alpine lakes (those located above the 2000 m tree line) are excellent sentinels of climate change as their chemistry and biology respond rapidly to environmental forcing. The Swiss alps are host to over 1500 alpine lakes, many of which have been newly mapped and thus never been studied2. Microorganisms play major ecological roles in these ecosystems, including primary production, cycling of elements, and attenuation of contaminants, but it is uncertain how physical climatic changes may affect microbial communities and their activities in alpine lakes. This project aims to: (i) record and monitor the unexplored microbial diversity in Swiss alpine lakes, and (ii) engage citizens in science and spread awareness about environmental conservation through participation in our field campaigns. In summary, 2000LAKES is a project of alpine citizen science aiming to understand the ecological impacts of climate change in alpine lakes and to promote the conservation of alpine microbial ecosystems joining forces between scientists and citizens.