Ice-covered periods might significantly contribute to lake emissions at ice-melt, yet a comprehensive understanding of under-ice carbon dioxide (CO2) dynamics is still lacking. This study investigated the processes driving spatiotemporal patterns of under-ice CO2 in large Lake Onego. In March 2015 and 2016, under-ice CO2, dissolved inorganic carbon (DIC), and dissolved organic carbon (DOC) distributions were measured along a river to an open-lake transect. CO2 decreased from 120/129 μmol L−1 in the river to 51/98 μmol L−1 in the bay, and 34/36 μmol L−1 in the open lake, while DOC decreased from 1.18/1.55 mmol L−1 in the river to 0.67/1.04 mmol L−1 in the bay in 2015 and 2016, respectively. These decreases in concentrations with increasing distance from the river mouth indicate that river discharge modulates spatial patterns of underice CO2. The variability between the 2 years was mainly driven by river discharge and ice transparency affecting the extent of under-ice convection. Higher discharge during winter 2016 resulted in higher CO2 concentrations in the bay. By contrast, intensive under-ice convection led to lower, more homogeneously distributed CO2 in 2015. In conclusion, the river-to-bay transition zone is characterized by strong CO2 variability and is therefore an important zone to consider when assessing the CO2 budget of large lakes.