Shallow thaw (thermokarst) lakes abundant in regions of permafrost-affected peatlands represent important sources of carbon dioxide and methane emission to the atmosphere, however the quantitative parameters of phytoplankton communities which control the C cycle in these lakes remain poorly known. This is especially true considering the roles of permafrost, hydrochemical composition of lakes, lake sizes and season as major governing factors on phytoplankton abundance and biodiversity. In this work, we quantified phytoplankton characteristics of 27 thermokarst lakes (sizes ranging from 115 m2 to 1.24 km2) sampled in spring, summer and autumn across a permafrost gradient (isolated, sporadic, discontinuous and continuous zone) in the Western Siberia Lowland (WSL). The biodiversity indices were highest during all seasons in lakes of the continuous permafrost zone and rather similar in lakes of isolated, sporadic and discontinuous permafrost zone. Considering all seasons and permafrost zones, the biomass and cell number of phytoplankton correlated with Dissolved Organic Carbon (DOC), phosphate, and some metal micro-nutrients (Ni, Zn). The strongest correlations were observed for Cyanophycea during summer, with pH, Ni, Cu, Zn, Sr, Ba (cell number) and Cu, Zn, Ba (biomass), and during autumn, with DOC, K, Cr, Cu, Zn, Ba, Cd, Pb (biomass). Using a substituting space for time approach for climate warming and permafrost thaw and suggesting a shift in permafrost boundaries northward, we foresee an increase in cell number and biomass in continuous permafrost zone in spring and summer, and a decrease in phytoplankton abundance in the discontinuous and sporadic permafrost zones. The biodiversity of phytoplankton in the continuous permafrost zone might decrease whereas in other zones, it may not exhibit any sizably change. However, in case of strong deepening of the active layer down to underlaying mineral horizons, and the release of some limiting nutrients (Si, P) due to enhanced connectivity of the lake with groundwater, the share of cyanobacteria and diatoms may increase.