Display omitted •Biodegradation preferentially decomposes the low molecular weight DOMs.•Aromatic and lignin fraction are accumulated in the mainstem.•Aquatic respiration of DOMs explain pCO2 levels in the post-wet and drought periods.•Terrestrial inputs are dominant pCO2 source in the initial-wet period.•pCO2 is positively correlated with DOM optical parameters. The mineralization of dissolved organic matter (DOM) can partially explain riverine carbon dioxide (CO2) emissions to the atmosphere. However, little is known about how the DOM origin and composition drive CO2 partial pressures (pCO2). Here, we reveal links between aquatic pCO2, DOM optical parameters (a254, a350 and S275-295 and S350-400) and nutrients in a subtropical river in China’s Dry-hot Valley Region. Biodegradation preferentially decomposed low molecular weight (LMW) DOMs, increasing high molecular weight (HMW) DOMs along the main stem. pCO2 was positively correlated with aromatic and lignin compounds, but negatively correlated with DOM molecular weight. Aquatic respiration of DOMs largely explained the pCO2 levels in the drought period, while terrestrial inputs were a pCO2 source in the initial-wet period. Our results illustrate how both DOM concentrations and speciation can explain pCO2 distribution and sources in rivers.