This article discusses the results of a taxonomic and ecological investigation into diatoms from polygonal ponds and quaternary permafrost deposits of Bol’shoy Lyakhovsky Island (New Siberian Archipelago) and the reconstruction of climatic changes on the island during Late Pleistocene/Holocene transition using fossil diatom assemblages from the permafrost deposits. The taxonomic list of diatoms includes 159 diatom species. The main ecological factors that determine the distribution of diatoms in the investigated data set are mean air temperature in July, рН, conductivity, water depth, and the concentration of Si4+ and Al3+. An increase in water depth and stable lacustrine conditions in the Lateglacial–Holocene in the ancient thermokarst lake relate to Lateglacial warming before 11860 ± 160 years BP and during the early Holocene between 11210 ± 160 and 7095 ± 60 years BP.