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<p>The Belo Monte hydropower complex located in the Xingu River is the largest run-of-the-river (ROR) hydroelectric system in the world and has one of the highest energy production capacities among dams. Its construction received significant media attention due to its potential social and environmental impacts. It is composed of two ROR reservoirs: the Xingu Reservoir (XR) in the Xingu's main branch and the Intermediate Reservoir (IR), an artificial reservoir fed by waters diverted from the Xingu River with longer water residence time compared to XR. We aimed to evaluate spatiotemporal variations in <span class="inline-formula">CO₂</span> partial pressure (<span class="inline-formula"><i>p</i>CO₂</span>) and <span class="inline-formula">CO₂</span> fluxes (<span class="inline-formula"><i>F</i>CO₂</span>) during the first 2 years after the Xingu River impoundment under the hypothesis that each reservoir has contrasting <span class="inline-formula"><i>F</i>CO₂</span> and <span class="inline-formula"><i>p</i>CO₂</span> as vegetation clearing reduces flooded area emissions. Time of the year had a significant influence on <span class="inline-formula"><i>p</i>CO₂</span> with the highest average values observed during the high-water season. Spatial heterogeneity throughout the entire study area was observed for <span class="inline-formula"><i>p</i>CO₂</span> during both low- and high-water seasons. <span class="inline-formula"><i>F</i>CO₂</span>, on the other hand, only showed significant spatial heterogeneity during the high-water period. <span class="inline-formula"><i>F</i>CO₂</span> (<span class="inline-formula">0.90±0.47</span> and <span class="inline-formula">1.08±0.62</span>&thinsp;<span class="inline-formula">µ</span>mol&thinsp;m<span class="inline-formula">²</span>&thinsp;d<span class="inline-formula">⁻¹</span> for XR and IR, respectively) and <span class="inline-formula"><i>p</i>CO₂</span> (<span class="inline-formula">1647±698</span> and <span class="inline-formula">1676±323</span>&thinsp;<span class="inline-formula">µ</span>atm for XR and IR, respectively) measured during the high-water season were on the same order of magnitude as previous observations in other Amazonian clearwater rivers unaffected by impoundment during the same season. In contrast, during the low-water season <span class="inline-formula"><i>F</i>CO₂</span> (<span class="inline-formula">0.69±0.28</span> and <span class="inline-formula">7.32±4.07</span>&thinsp;<span class="inline-formula">µ</span>mol&thinsp;m<span class="inline-formula">²</span>&thinsp;d<span class="inline-formula">⁻¹</span> for XR and IR, respectively) and <span class="inline-formula"><i>p</i>CO₂</span> (<span class="inline-formula">839±646</span> and <span class="inline-formula">1797±354</span>&thinsp;<span class="inline-formula">µ</span>atm for XR and IR, respectively) in IR were an order of magnitude higher than literature <span class="inline-formula"><i>F</i>CO₂</span> observations in clearwater rivers with naturally flowing waters. When <span class="inline-formula">CO₂</span> emissions are compared between reservoirs, IR emissions were 90&thinsp;% higher than values from the XR during low-water season, reinforcing the clear influence of reservoir characteristics on <span class="inline-formula">CO₂</span> emissions. Based on our observations in the Belo Monte hydropower complex, <span class="inline-formula">CO₂</span> emissions from ROR reservoirs to the atmosphere are in the range of natural Amazonian rivers. However, the associated reservoir (IR) may exceed natural river emission rates due to the preimpounding vegetation influence. 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 <span class="inline-formula"><i>F</i>CO₂</span> over their entire life cycle in order to improve estimates of <span class="inline-formula">CO₂</span> emissions per kilowatt for hydropower projects planned for tropical rivers.</p>