Siberian larch forests growing on shallow permafrost soils have not, until now, been considered as controlling the abiotic and biotic characteristics of the vast number of thaw-lake ecosystems. We show, using four independent data-sets (a modern data-set from 201 lakes from tundra to taiga, and three lake-core records), that lake-water geochemistry in Yakutia is highly correlated with vegetation. Alkalinity increases with catchment forest density. We postulate that in this arid area, higher evapotranspiration in larch forests compared to tundra vegetation leads to local salt accumulation in soils. Solutes are transported to nearby thaw-lakes during rain-events and snow-melt, but are not fully transported into rivers because there is no continuous groundwater-flow within permafrost soils. This implies that potentially large shifts in the chemical characteristics of aquatic ecosystems to known warming are absent because of the slow response of catchment forests to climate change.