Modern research proves the need to include waterbodies in regional and global models of carbon exchange. The concentration of carbon dioxide in surface waters is generally higher than equilibrium with a partial atmospheric pressure of 400 µatm allows. The study of the functioning and regional role of aquatic systems, especially regard to inorganic carbon dynamics, is insufficient, especially in circumboreal regions. The review highlights the theoretical foundations and relevance of studies of dissolved carbon dioxide; methodological approaches in assessing this indicator, as well as the role of dissolved CO2 in natural waters of boreal and arctic regions. Soil organic matter and dissolved carbon dioxide are the main sources of CO2 in surface waters, but this contribution has not yet been quantified. This is due to the underestimation of the abiotic aspects of soil gas exchange, the absolute predominance of studies of gas exchange at the soil-atmosphere interface without taking into account the interaction with groundwater, as well as methodological difficulties in measuring gas concentrations in soil-ground and surface waters. Instrumental measurement methods are not standardized, and the calculated ones have very high systematic and analytical errors. The conclusion points to the need to study the hydrological continuum: from source (terrestrial ecosystems) to large rivers and lakes, with particular attention to the incorporation of CO2 from groundwater into the carbon budget of the entire watershed.