A large fraction of the organic carbon derived from land that is transported through inland waters is decomposed along river systems and emitted to the atmosphere as carbon dioxide (CO2). The Amazon River outgasses nearly as much CO2 as the rainforest sequesters on an annual basis, representing ~25% of global CO2 emissions from inland waters. However, current estimates of CO2 outgassing from the Amazon basin are based on a conservative upscaling of measurements made in the central Amazon, meaning both basin and global scale budgets are likely underestimated. The lower Amazon River, from Óbidos to the river mouth, represents ~13% of the total drainage basin area, and is not included in current basin-scale estimates. Here, we assessed the concentration and evasion rate of CO2 along the lower Amazon River corridor and its major tributaries, the Tapajós and Xingu Rivers. Evasive CO2 fluxes were directly measured using floating chambers and gas transfer coefficients (k600) were calculated for different hydrological seasons. Temporal variations in pCO2 and CO2 emissions were similar to previous observations throughout the Amazon (e.g. peak concentrations at high water) and CO2 outgassing was lower in the clearwater tributaries compared to the mainstem. However, k600 values were higher than previously reported upstream likely due to the generally windier conditions, turbulence caused by tidal forces, and an amplification of these factors in the wider channels with a longer fetch. We estimate that the lower Amazon River mainstem emits 0.2 Pg C yr-1 within our study boundaries, or as much as 0.48 Pg C yr-1 if the entire spatial extent to the geographical mouth is considered. Including these values with updated basin scale estimates and estimates of CO2 outgassing from small streams we estimate that the Amazon running waters outgasses as much as 1.39 Pg C yr-1, increasing the global emissions from inland waters by 43% for a total of 2.9 Pg C yr-1. These results highlight a large missing gap in basin-scale carbon budgets along the complete continuum of the Amazon River, and likely most other large river systems, that could drastically alter global scale carbon budgets.

Here we present direct measurements of the biological breakdown of ¹³C‐labeled substrates to CO₂ at seven locations along the lower Amazon River, from Óbidos to the mouth. Dark incubation experiments were performed at high and low water periods using vanillin, a lignin phenol derived from vascular plants, and at the high water period using four different ¹³C‐labeled plant litter leachates. Leachates derived from oak wood were degraded most slowly with vanillin monomers, macrophyte leaves, macrophyte stems, and whole grass leachates being converted to CO₂ 1.2, 1.3, 1.7, and 2.3 times faster, respectively, at the upstream boundary, Óbidos. Relative to Óbidos, the sum degradation rate of all four leachates was 3.3 and 2.6 times faster in the algae‐rich Tapajós and Xingu Rivers, respectively. Likewise, the leachates were broken down 3.2 times more quickly at Óbidos when algal biomass from the Tapajós River was simultaneously added. Leachate reactivity similarly increased from Óbidos to the mouth with leachates breaking down 1.7 times more quickly at Almeirim (midway to the mouth) and 2.8 times more quickly across the river mouth. There was no discernible correlation between in situ nutrient levels and remineralization rates, suggesting that priming effects were an important factor controlling reactivity along the continuum. Further, continuous measurements of CO₂, O₂, and conductivity along the confluence of the Tapajós and Amazon Rivers and the Xingu and Jarauçu Rivers revealed in situ evidence for enhanced O₂ drawdown and CO₂ production along the mixing zone of these confluences.

Most measurements of respiration rates in large tropical rivers do not account for the influence of river flow conditions on microbial activity. We developed a ship‐board spinning incubation system for measuring O₂ drawdown under different rotation velocities and deployed the system along the lower Amazon River during four hydrologic periods. Average respiration rates in incubation chambers rotated at 0.22 m s⁻¹ and 0.66 m s⁻¹ were 1.4 and 2.4 times higher than stationary chambers, respectively. On average, depth‐integrated respiration rates in chambers spun at 0.22 m s⁻¹ and 0.66 m s⁻¹ accounted for 64% ± 22% and 104% ± 36% of CO₂ outgassing rates, respectively, in mainstem sites. Continuous measurements of in situ pCO₂ were also made along with cross‐channel profiles of river velocity. A positive correlation between river velocity and pCO₂ was observed along the lower river (r² = 0.67–0.96) and throughout a tidal cycle.

Coloured dissolved organic matter (CDOM) is one of the major contributors to the absorption budget of most freshwaters and can be used as a proxy to assess non-optical carbon fractions such as dissolved organic carbon (DOC) and the partial pressure of carbon dioxide (pCO₂). Nevertheless, riverine studies that explore the former relationships are still relatively scarce, especially within tropical regions. Here we document the spatial-seasonal variability of CDOM, DOC and pCO₂, and assess the potential of CDOM absorption coefficient (a_CDOM(412)) for estimating DOC concentration and pCO₂ along the Lower Amazon River. Our results revealed differences in the dissolved organic matter (DOM) quality between clearwater (CW) tributaries and the Amazon River mainstream. A linear relationship between DOC and CDOM was observed when tributaries and mainstream are evaluated separately (Amazon River: N = 42, R² = 0.74, p<0.05; CW: N = 13, R² = 0.57, p<0.05). However, this linear relationship was not observed during periods of higher rainfall and river discharge, requiring a specific model for these time periods to be developed (N = 25, R² = 0.58, p<0.05). A strong linear positive relation was found between a_CDOM(412) and pCO₂(N = 69, R² = 0.65, p<0.05) along the lower river. pCO₂ was less affected by the optical difference between tributaries and mainstream waters or by the discharge conditions when compared to CDOM to DOC relationships. Including the river water temperature in the model improves our ability to estimate pCO₂ (N = 69; R² = 0.80, p<0.05). The ability to assess both DOC and pCO₂ from CDOM optical properties opens further perspectives on the use of ocean colour remote sensing data for monitoring carbon dynamics in large running water systems worldwide.