The ponds and small reservoirs have a large number and wide distribution across China, and are thus an important component in the accounting of carbon balance. With the increasing eutrophication of these water bodies, the carbon emission processes changed considerable, increasing the uncertainty of calculating carbon emission fluxes of ponds/reservoirs. This study took two ponds and three reservoirs in the Zhuxi River Basin as the study areas. A nine-month monitoring of CO₂ and CH₄ fluxes was conducted at the water-air interface. Based on the monitoring results, the study investigated the impacts of eutrophication on CO₂ and CH₄ emissions in these small water bodies. The results showed that the average CO₂ and CH₄ emission fluxes were highest in the moderately eutrophic ponds/reservoirs, followed by lightly eutrophic ponds/reservoirs, and lowest in mesotrophic ponds/reservoirs. In mesotrophic ponds/reservoirs, the average CO₂ and CH₄ emission fluxes at the water-air interface were 17.32 and 0.42 mmol/(m² ·d), respectively. In lightly eutrophic ponds/reservoirs, the average CO2 and CH4 emission fluxes were 17.89 and 0.48 mmol/(m² ·d), respectively. In moderately eutrophic ponds/reservoirs, the average CO2 and CH₄ emission fluxes were 19.37 and 0.78 mmol/(m² ·d), respectively. Overall, the study found that these water bodies acted as sources of CO₂ and CH₄ . The CO₂ and CH₄ emission fluxes were influenced by various factors, including temperature, dissolved oxygen, and pH. With the increase in eutrophication of small water bodies, the emission fluxes of CO₂ and CH₄ howed a nonlinear increasing trend. The CH₄ emission flux in moderately eutrophic water bodies was approximately twice that of mesotrophic waters, indicating that controlling eutrophication could effectively decrease greenhouse gas emission such as CH₄ from water bodies. Therefore, to accurately estimate and predict greenhouse gas emissions such as CO₂ and CH₄ from small water bodies, eutrophication should be considered as a potential influencing factor.