Abstract. Despite relatively good knowledge of the biogeochemistry of Siberian thermokarst lakes during summer base flow, their seasonal dynamics remains almost unexplored. This work describes the chemical composition of ~130 thermokarst lakes ranging in size from a few m² to several km², located in the discontinuous permafrost zone. Lakes were sampled during spring flood, just after the ice break (early June), the end of summer (August), the beginning of ice formation (October) and during the full freezing season in winter (February). The lakes larger than 1000 m² did not exhibit any statistically significant control of the lake size on dissolved organic carbon (DOC), the major and trace element concentrations over three major open water seasons. On the annual scale, the majority of dissolved elements including organic carbon increased their concentration from 30 to 500%, with a statistically significant (p < 0.05) trend from spring to winter. The concentrations of most trace elements (TEs) increased in the order spring > summer > autumn > winter. The ice formation in October included several stages: first, surface layer freezing followed by crack (fissure) formation with unfrozen water from the deeper layers spreading over the ice surface. This water was subsequently frozen and formed layered ice rich in organic matter. As a result, the DOC and metal (Mn, Fe, Ni, Cu, Zn, As, Ba and Pb) concentrations were highest near the surface of the ice column (0 to 20 cm) and decreased by a factor of 2 towards the bottom. The main implications of discovered freeze-driven solute concentrations in thermokarst lake waters are enhanced colloidal coagulation and removal of dissolved organic matter and associated insoluble metals from the water column to the sediments. The measured distribution coefficients of a TE between amorphous organo-ferric coagulates and lake water (<0.45 μm) were similar to those reported earlier for Fe-rich colloids and low molecular weight (<1 kDa, or <1–2 nm) fractions of thermokarst lake waters, suggesting massive co-precipitation of TE with amorphous Fe oxyhydroxide stabilized by organic matter. Although the concentration of most elements was lowest in spring, this period of maximal water coverage of land created a significant reservoir of DOC and soluble metals in the water column that can be easily mobilized to the hydrological network. The highest DOC concentration observed in the smallest (<100 m²) water bodies in spring suggests their strongly heterotrophic status and, therefore, a potentially elevated CO₂ flux from the lake surface to the atmosphere.