This dataset contains dissolved inorganic/organic carbon (DIC/DOC) concentrations, its stable isotope ratios (δ13CDIC/DOC), partial pressure of carbon dioxide in the water column pCO₂(aq) (pCO2(aq)) and area-integrated CO₂ emission rates derived from flux calculations (FCO2; g C d⁻¹), along with corresponding parameters (temperature, pH, calcium, bicarbonate) collected from the Danube River and its key tributaries during five seasonal sampling campaigns in 2023 and 2024. Water samples were collected using a weighted 2 L sampling bottle submerged 1–2 meters below the surface, with sampling conducted from the river center via bridges or passenger boats, and occasionally from the riverbank. In situ temperature measurements were taken with a multiparameter instrument (HQ40d, HACH™, Loveland, CO, USA). δ13ODIC/DOC was analyzed using a OI Analytical Aurora 1030W-IRMS. This dataset is providing valuable insights into carbon dynamics in a large river system and support investigations of biogeochemical cycling. It further can inform ecosystem management and conservation strategies under changing environmental conditions.