Water surface greenhouse gas (GHG) emissions in freshwater reservoirs are closely related to limnological processes in the water column. Affected by both reservoir operation and seasonal changes, variations in the hydro-morphological conditions in the river–reservoir continuum will create distinctive patterns in water surface GHG emissions. A one-year field survey was carried out in the Pengxi River–reservoir continuum, a part of the Three Gorges Reservoir (TGR) immediately after the TGR reached its maximum water level. The annual average water surface CO2and CH4emissions at the riverine background sampling sites were 6.23 ± 0.93 and 0.025 ± 0.006 mmol h−1 m−2, respectively. The CO2emissions were higher than those in the downstream reservoirs. The development of phytoplankton controlled the downstream decrease in water surface CO2emissions. The presence of thermal stratification in the permanent backwater area supported extensive phytoplankton blooms, resulting in a carbon sink during several months of the year. The CH4emissions were mainly impacted by water temperature and dissolved organic carbon. The greatest water surface CH4emission was detected in the fluctuating backwater area, likely due to a shallower water column and abundant organic matter. The Pengxi River backwater area did not show significant increase in water surface GHG emissions reported in tropical reservoirs. In evaluating the net GHG emissions by the impoundment of TGR, the net change in the carbon budget and the contribution of nitrogen and phosphorus should be taken into consideration in this eutrophic river–reservoir continuum. © 2017, Springer International Publishing Switzerland.