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Description: Lake Baikal has been experiencing limnological changes from recent atmospheric warming since the 1950s, with rising lake water temperatures, reduced ice cover duration and reduced lake water mixing due to stronger thermal stratification. This study uses lake sediment cores to reconstruct recent changes (c. past 20 years) in Lake Baikal’s pelagic diatom communities relative to previous 20th century diatom assemblage records collected in 1993 and 1994 at the same locations in the lake. Recent changes documented within the core-top diatom records are in agreement with predictions by Mackay et al (2006) and Moore et al (2009) of diatom responses to warming at Lake Baikal. Sediments in the south basin of the lake exhibit clear temporal changes, with the most rapid occurring in the 1990’s with shifts towards higher abundances of the cosmopolitan Synedra acus and a decline in endemic species, mainly Cyclotella minuta and Stephanodiscus meyerii and to a lesser extent Aulacoseira baicalensis and Aulacoseira skvortzowii. The north basin, in contrast, shows no evidence of recent diatom response to lake warming despite marked declines in north basin ice cover in recent decades. This study also shows no diatom-inferred evidence of eutrophication from deep water sediments. However, due to the localised impacts seen in areas of Lake Baikal’s shoreline from nutrient pollution derived from out-dated sewage treatment plants, urgent action is vital to prevent anthropogenic pollution extending into the open waters.