Lake Baikal is the World s oldest, deepest and largest (by volume) lake and contains many endemic species. Since 1996, after becoming a UNESCO World Heritage Area, the effects of global warming and local anthropogenic eutrophication on its unique ecosystem become a subject of international discussion. Phytoplankton pigments monitor changes of the phytoplankton composition and productivity and thereby changes of climatic and other environmental conditions. An intense phytoplankton monitoring was carried out in conjunction with a local long-term monitoring programme; the pigment flux through the water column was determined and how the main phytoplankton groups were represented in the deposited material; the work shows furthermore how sedimentary pigments can be used to assess the phytoplankton response to natural climate changes in the pristine lake. The work is directed to scientists, environmentalists and decision makers.