Fossil diatom assemblages in a sediment core from a small lake in Central Kamchatka (Russia) were used to reconstruct palaeoenvironmental conditions of the late Holocene. The waterbody may be a kettle lake that formed on a moraine of the Two-Yurts Lake Valley, located on the eastern slope of the Central Kamchatka Mountain Chain. At present, it is a seepage lake with no surficial outflow. Fossil diatom assemblages show an almost constant ratio between planktonic and periphytic forms throughout the record. Downcore variations in the relative abundances of diatom species enabled division of the core into four diatom assemblage zones, mainly related to changes in abundances of Aulacoseira subarctica, Stephanodiscus minutulus, and Discostella pseudostelligera and several benthic species. Associated variations in the composition and content of organic matter are consistent with the diatom stratigraphy. The oldest recovered sediments date to about 3220 BC. They lie below a sedimentation hiatus and likely include reworked deposits from nearby Two-Yurts Lake. The initial lake stage between 870 and 400 BC was characterized by acidic shallow-water conditions. Between 400 BC and AD 1400, lacustrine conditions were established, with highest contributions from planktonic diatoms. The interval between AD 1400 and 1900 might reflect summer cooling during the Little Ice Age, indicated by diatoms that prefer strong turbulence, nutrient recycling and cooler summer conditions. The timing of palaeolimnological changes generally fits the pattern of neoglacial cooling during the late Holocene on Kamchatka and in the neighbouring Sea of Okhotsk, mainly driven by the prevailing modes of regional atmospheric circulation. © 2012 Springer Science+Business Media B.V.