Diatom assemblages and limnological data were analyzed from 74 lakes spanning arctic treeline in three geographical regions of northern Russia: near the mouth of the Pechora River, on the Taimyr Peninsula, and near the mouth of the Lena River. Analysis of similarities indicated that diatom assemblages in tundra and forest lakes were significantly different from each other in all regions, with tundra lakes generally associated with higher abundances of small benthic Fragilaria Lyngbye taxa. Canonical correspondence analysis identified variables related to ion concentrations (e.g. Na+, dissolved inorganic carbon), lake depth, silica concentrations, and surface water temperatures as factors that explained significant amounts of variation in the diatom assemblages. Across treeline, the generally higher surface water temperatures of the forested lakes consistently accounted for a significant proportion of the diatom distribution patterns. Major ion concentrations also explained significant amounts of variation in the diatom assemblages across treeline for all three regions; however, regional trends were most likely influenced by local factors (i.e. ocean proximity or anthropogenic activities). The importance of climatic gradients across treeline (e.g. temperature) diatom distributions provides additional evidence that diatoms may be useful as paleoclimatic indicators. However, combination of the three calibration sets revealed that local water chemistry determinants (e.g. lithology, marine influence) overrode the influence of climatic gradients in explaining diatom distributions, suggesting that regional differences must be minimized for successful combination of geographically separate calibration sets.