This dataset contains alkalinity, dissolved inorganic carbon (DIC) and dissolved organic carbon (DOC) concentrations, d13C values of DIC, DOC, and particulate organic carbon (POC), d18O values of dissolved oxygen, and calculated partial pressure of CO2 (pCO2), CO2 fluxes, and gas-transfer velocity (k600) from stream-water samples collected at 13 sites along the first 3.25 km of the Wiesent karst headwater stream in northern Bavaria, Germany, from March 2023 to May 2024. The dataset supports analyses of carbonate-system dynamics, oxygen cycling, and CO2 evasion under varying hydroclimatic conditions.