The oxygen isotope composition of diatom silica (d18Odiatom) from marine and lake sediments is helpful for the interpretation of the past climate and environments, especially when complemented by other proxy records. This paper presents a Holocene oxygen isotope record of diatoms from Lake Kotokel, located 2 km east of Lake Baikal in southern Siberia, Russia. The isotope record displays variations in d18Odiatom from +23.7 to +30.3‰ from about 11.5 ka BP until today. Comparing the isotope composition of recent Lake Kotokel water (mean d18O = -12‰) to that of the most recent diatom sample (d18O = +27.5‰), an isotope fractionation in the right order of magnitude was calculated. The Kotokel d18O diatom record is rather controlled by changes in the isotopic composition of the lake water rather than by lake temperature. Lake Kotokel is a dynamic system triggered by differential environmental changes closely linked with various lake-internal hydrological factors. A continuous depletion in d18O of 6.6‰ is observed from Early to Late Holocene, which is in line with other hemispheric environmental changes (i.e. a Mid- to Late Holocene cooling). Enhanced evaporation effects and higher relative supply from a southerly moisture source explain the relatively heavy isotopic composition in a rather cold Early Holocene. In summary, changes in the Holocene d18O diatom record of Lake Kotokel reflect variations in d18O of precipitation linked with both Tair as well as evaporation effects and, to a lesser degree, meltwater pulses from the mountainous hinterland and changing atmospheric moisture sources.