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Lake Baikal is the oldest, deepest, and most voluminous freshwater lake on Earth. Despite its enormous depth, episodically (almost twice a year) large amounts of surface, cold, and oxygenated water sink until the bottom of the lake due to thermobaric instability, with consequent effects on the ecology of the whole lake. A minimal one-dimensional model is used to investigate how changes in the main external forcing (i.e., wind and lake surface temperature) may affect this deep ventilation mechanism. The effect of climate change is evaluated considering the IPCC RCP8.5 and some idealized scenarios and is quantified by (i) estimating the mean annual downwelling volume and temperature and (ii) analyzing vertical temperature and dissolved oxygen profiles. The results suggest that the strongest impact is produced by alterations of wind forcing, while deep ventilation is resistant to rising lake surface temperature. In fact, the seasons when deep ventilation can occur can be shifted in time by lake warming, but not dramatically modified in their duration. Overall, the results show that Lake Baikal is sensible to climate change, to an extent that the ecosystem and water quality of this unique lacustrine system may undergo profound disturbances.