<p><strong>Abstract.</strong> River damming alters local hydrology, which influences aspects of the carbon cycle such as carbon dioxide (CO<sub>2</sub>) production and emissions. Run-of-the-river reservoirs (RORs) are designed to have a smaller flooded area than traditional storage reservoirs, maintaining a river flow similar to natural seasonal water level fluctuation. These features may potentially reduce the impacts of the dam on the natural carbon cycle. However, little information on the influence of RORs on the carbon cycle is available, especially for the Amazon or other large tropical rivers. The Belo Monte hydropower complex is a large ROR located in the Xingu River, a clearwater tributary of the Amazon River. It is composed of two reservoirs; the Xingu Reservoir (XR) with ROR characteristics and the Intermediate Reservoir (IR) with storage reservoir traits. Here we evaluate spatiotemporal variation of surface water CO<sub>2</sub> partial pressure (pCO<sub>2</sub>), CO<sub>2</sub> fluxes (FCO<sub>2</sub>), and gas exchange coefficients (k600) during the first two years after the impoundment of the Xingu River. Seasonal changes in the water level had a significant influence on pCO<sub>2</sub> with the highest average values observed during high water. The FCO<sub>2</sub> was more variable, although correlated with pCO<sub>2</sub>, throughout the two first years of river impoundment. Spatial heterogeneity was observed for pCO<sub>2</sub> during both seasons while FCO<sub>2</sub> showed significant spatial heterogeneity only during the high water period. High water FCO<sub>2</sub> and pCO<sub>2</sub> values were on the same order of magnitude as emissions measured in Amazonian clearwater rivers unaffected by impoundment, but low water values were an order of magnitude higher than previous observations in clearwater rivers with natural flowing waters. Finally, we observed variability in CO<sub>2</sub> fluxes related to the type of environment (i.e., river channel, downstream the dams, outside reservoirs and flooded areas), among reservoirs and the land use of flooded areas after impoundment of the Belo Monte hydropower complex. For example, CO<sub>2</sub> emissions were 15 % and 90 % higher for the IR compared to XR during high and low water season, respectively, indicating that storage reservoirs may be larger sources of CO<sub>2</sub> to the atmosphere compared to RORs. Since many reservoirs are still planned to be constructed in the Amazon and throughout the world, it is critical to evaluate the implications of reservoir traits on CO<sub>2</sub> fluxes over their entire life cycle in order to generate energy that has lower emissions per KW.</p>