Diatoms in Lake Baikal exhibit significant spatial variation, related to prevailing climate, lake morphology and fluvial input into the lake. Here we have assessed the threats to endemic planktonic diatom species (through the development of empirical models), which form a major component of primary production within the lake. Multivariate techniques employed include redundancy analysis (RDA) and Huisman–Olff–Fresco (HOF) models. Our analyses suggest that eight environmental variables were significant in explaining diatom distribution across the lake, and in order of importance these are snow thickness on the ice, water depth, duration of days with white ice, suspended matter in the lake, days of total ice duration, temperature of the water surface in July, concentration of zooplankton and suspended organic matter. Impacts on dominant phytoplankton diatom species are highlighted using t-value biplots. Predictions of future climate change on Lake Baikal are likely to result in shorter periods of ice cover, decreased snow cover across the lake in spring, increased fluvial input into the lake, and an increase in the intensification of surface water stratification during summer months. All these factors are likely to impact negatively on the slow-growing, cold-water endemics such as Aulacoseira baicalensis and Cyclotella minuta, which currently dominate diatom assemblages. Instead, taxa that are only intermittently abundant, at present, in offshore areas (e.g. Stephanodiscus meyerii) are likely to become more frequent. However, given the climatic gradient across the lake, the timing and extent of changes in community structure are likely to vary. Moreover, palaeolimnological records show that Lake Baikal diatom assemblages have been dynamic throughout the Holocene, with both endemic and cosmopolitan species exhibiting periods of dominance. Effects of climate change on the entire lake ecosystem may yet be profound as the structure of the pelagic food web may change from one based on endemic diatom taxa to one dominated by nondiatom picoplankton, and as limnological functioning (e.g. stratification and mixing) affects deepwater oxygen availability, nutrient cycling and trophic linkages.