Impounding has greatly altered carbon cycle in rivers. To quantify this effect, we measured CO<sub>2</sub> effluxes from a mountainous valley-type reservoir in the upper Mekong River (Lancang River in China) and compared with those from the pristine river channel. Evasion rates from reservoir surface was 408 mg m<sup>−2</sup> d<sup>−1</sup> and 305 mg m<sup>−2</sup> d<sup>−1</sup> in the dry season and rainy season respectively, much lower than those from river channel of 2168 mg m<sup>−2</sup> d<sup>−1</sup> and 374 mg m<sup>−2</sup> d<sup>−1</sup>. Lower efflux in the rainy season deviated from the traditional theory that rainfalls can bring more organic carbon for mineralization and increase the efflux. The analysis found that efflux was closely related to the physical mixing process of inflow and reservoir water. The light overflow rich in CO<sub>2</sub> in dry season contact the atmosphere directly and release more gases while the underflow in warm wet season leaved insufficient time for mineralization and hardly support high efflux in surface water. Evasion rate at the downstream of the dam was also limited due to surface water withdrawal. Lastly, the littoral zone was found to be a hotspot for CO<sub>2</sub> emission despite its limited area leading to its negligible contribution in total annual emission rate. In contrast, diurnal efflux variability in the littoral zone indicates that the effluxes were significantly higher at night than in the daytime, which increased the annual emission rate to by a half.