Inland waters are vital sinks for active carbon (C) and potential sources of greenhouse gas emissions. In this study, the characteristics of dissolved carbon dioxide (CO₂) and methane (CH₄) concentrations in the Nantiaoxi River system in the upper reaches of the Taihu Lake basin were observed between Jul. 2019 and Nov. 2019 (summer and autumn) using headspace equilibration-gas chromatography. Simultaneously, physical and chemical parameters were also determined to understand the factors influencing dissolved CO₂ and CH₄ concentrations. The results showed that the mean dissolved CO₂ concentrations and saturation levels in water were (505.47±16.99) μg·L^-1 and (256.31±8.32)%, respectively, and the corresponding values for CH₄ were (1.88±0.09) μg·L^-1 and (5218.74±264.30)%, respectively. The saturation levels of dissolved CO₂ and CH₄ at all observation points were greater than 100%, indicating that the Nantiaoxi River system is a potential source of CO₂ and CH₄. The highest mean dissolved CO₂ concentrations in water were found in agricultural areas followed by residential and forest areas, and there were significant differences among the three land-use types. The mean dissolved CH₄ concentrations in the water in residential areas were significantly higher than those in agricultural area forest areas. The dissolved CO₂ concentrations, saturation levels of CO₂, dissolved CH₄ concentrations, and saturation levels of CH₄ in water were all negatively correlated with oxidation reduction potential (ORP) (P<0.01) and positively correlated with electrical conductivity (EC) (P<0.01). The discrepancies in chlorophyll (Chl-a), nitrate (NO₃^--N), total nitrogen (TN), and EC were the main reasons for differences in dissolved CO₂ concentrations among the different land use types. Phytoplankton growth could be promoted by the higher input of nitrogen pollutants into rivers in agricultural and residential areas, and respiration could be also enhanced, resulting in higher dissolved CO₂ concentrations. The higher concentrations of dissolved organic carbon (DOC) and ammonium nitrogen (NH₄⁺-N) in the water, and the water temperature in residential areas, were probably the main causes of the higher dissolved CH₄ concentrations. Rainfall also had some influence on dissolved CO₂ and CH₄ concentrations in the water associated with the different land use types. Specifically, higher concentrations of nitrogen pollutants and the enhancement of DOC were the main drivers of high dissolved CO₂ concentrations in agricultural areas as well as the higher dissolved CH₄ concentrations in residential areas following rainfall events.