Permafrost thaw in continental lowlands produces large number of thermokarst (thaw) lakes, which act as amajor regulator of carbon (C) storage in sediments and C emission in the atmosphere. Here we studied thawlakes of the NE European permafrost peatlands - shallow water bodies located within frozen peat bogs and re-ceiving the majority of their water input from lateral (surface) runoff.Wealsoconductedmesocosm experimentsvia interacting lake waters with frozen peat and dominant ground vegetation - lichen and moss. There was a sys-tematic decrease in concentrations of dissolved C, CO2, nutrients and metals with an increase in lake size, corre-sponding to temporal evolution of the water body and thermokarst development. We hypothesized that groundvegetation andfrozen peat provide the majorityof C, nutrientsand inorganicsolutes in the water columnof theselakes, and that microbial processing of terrestrial organic matter controls the pattern of CO2and nutrient concen-trations in thermokarst lakes. Substrate mass-normalized C, nutrient (N, P, K), major and trace metal release wasmaximal in moss mesocosms. Afterfirst 16 h of reaction, the pCO2increased ten-fold in mesocosms with mossand lichen; this increase was much less pronounced in experiments with permafrost peat. Overall, moss and li-chen were the dominant factors controlling the enrichment of the lake water in organic C, nutrients, and tracemetals and rising the CO2concentration. The global significance of obtained results is that the changes in groundvegetation, rather than mere frozen peat thawing, may exert the primary control on C, major and trace elementbalance in aquatic ecosystems of tundra peatlands under climate warming scenario.