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The carbon (C) cycle in inland waters, including carbon concentrations in and carbon dioxide (CO2) emissions from water surfaces, are at the forefront of biogeochemical studies, especially in regions strongly impacted by ongoing climate change. Towards a better understanding of C storage, transport and emission in Central Asian mountain regions, an area of knowledge that has been extremely poorly studied until now, here, we carried out systematic measurements of dissolved C and CO2 emissions in rivers and lakes located along a macrotransect of various natural landscapes in the Sayan–Altai mountain region, from the high mountains of the Western Sayan in the northwest of Tyva to the arid (dry) steppes and semideserts in the intermountain basins in the southeast of Tyva on the border with Mongolia. New data on major hydrochemical parameters and CO2 fluxes (fCO2) gathered by floating chambers and dissolved organic and inorganic carbon (DOC and DIC, respectively) concentrations collected over the four main hydrological seasons allowed us 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 permafrost, river watershed size, lake area and climate parameters as well as 'internal' biogeochemical drivers (pH, mineralization, organic matter quality and bacterial population) on CO2 concentration and emissions in lakes and rivers of this region and compared them with available data from other subarctic and mountain settings. We found strong environmental control of the CO2 pattern in the studied water bodies, with thermokarst lakes being drastically different from other lakes. In freshwater lakes, pCO2 negatively correlated with O2, whereas the water temperature exerted a positive impact on pCO2 in large rivers. Overall, the large complexity of counteracting external and internal drivers of CO2 exchange between the water surfaces and the atmosphere (CO2-rich underground DIC influx and lateral soil and subsurface water; CO2 production in the water column due to dissolved and particulate OC biodegradation; CO2 uptake by aquatic biota) precluded establishing simple causalities between a single environmental parameter and the fCO2 of rivers and lakes. The season-averaged CO2 emission flux from the rivers of Tyva measured in this study was comparable, with some uncertainty, to the C uptake fluxes from terrestrial ecosystems of the region, which were assessed in other works. [ABSTRACT FROM AUTHOR]