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Lake Sevan is the largest freshwater body in the Caucasus region, situated at an altitude of 1,900 m asl. While it is a major water resource in the whole region, Lake Sevan has received little attention in international limnological literature. Although recent studies pointed to algal blooms and negative impacts of climate change and eutrophication, the physical controls on thermal dynamics have not been characterized and model-based assessments of climate change impacts are lacking. We compiled a decade of historical data for meteorological conditions and temperature dynamics in Lake Sevan and used a one-dimensional hydrodynamic model (GLM 3.1) in order to study thermal structure, the stratification phenology and their meteorological drivers in this large mountain lake. We then evaluated the representativeness of meteorological data products covering almost 4 decades (EWEMBI-dataset: 1979-2016) for driving the model and found that these data are well suited to restore long term thermal dynamics in Lake Sevan. This established model setting allowed us to identify major changes in Lake Sevan’s stratification in response to changing meteorological conditions as expected from ongoing climate change. Our results point to a changing mixing type from dimictic to monomictic as Lake Sevan will experience prolonged summer stratification periods and more stable stratification. These projected changes in stratification must be included in long-term management perspectives as they will intensify water quality deteriorations like surface algal blooms or deep water anoxia.