Carbon (C) cycle n inland waters, including its concentrations and carbon dioxide (CO2) emis-sions from water surfaces are at the forefront of biogeochemical studies, especially in the re-gions, strongly impacted by on-going climate change. Towards better understanding of C stor-age, transport and emission in Central Asian mountain regions, extremely poorly studied until now, here we carried out systematic measurements of dissolved C and CO2 emissions in 15 riv-ers and 5 lakes located along a macro-transect of various natural landscapes in the Sayan-Altai mountain region, from high mountains of the Western Sayan in the northwest of Tyva to arid (dry) steppe and semi-deserts in intermountain basins of the southeast of Tyva, the border with Mongolia. New data on major hydrochemical parameters, CO2 fluxes by floating chambers, dis-solved organic and inorganic carbon concentrations collected over four main hydrological sea-sons allowed to assess the current C biogeochemical status of these water bodies in order to judge possible future changes under climate warming. We further tested the impact of perma-frost, river watershed size, lake area and climate parameters as well as ‘internal’ biogeochemical drivers (pH, mineralization, organic matter quality and bacterial population) on CO2 concentra-tion and emissions in lakes and rivers of this region, and compared them with available data on other subarctic and mountain settings.