<p dir="ltr">This dataset contains concentrations of three dissolved greenhouse gases (GHGs) - carbon dioxide (CO<sub>2</sub>), methane (CH<sub>4</sub>), and nitrous oxide (N<sub>2</sub>O) - collected from the lower reaches of the Zhongtian River in southeast China. The data were obtained through two complementary sampling schemes: monthly sampling and diel (24-hour) sampling.</p><p dir="ltr">The core of the dataset comes from monthly sampling campaigns conducted over three years: 2018 (representing the period with wetlands) and 2021-2022 (representing the period after wetland clearance in late 2019). Samples were collected at four sites (S0-S3), facilitating a direct comparison of GHG dynamics before and after the wetland removal. For the monthly data, estimated diffusive GHG fluxes are also included. Additionally, the dataset includes diel sampling data from two 24-hour campaigns (July 2018 and August 2021) conducted at a specific reach. These data capture the hourly variation of dissolved GHGs as water passed through the area under contrasting wetland conditions. Gas samples were analyzed using the headspace equilibration technique followed by gas chromatography.</p>