Dispersed and unknown pollution sources complicate water management in large transboundary watersheds. We applied stable isotopes of water and nitrate together with contaminants of emerging concern (CECs: carbamazepine, caffeine, sulfamethoxazole, perfluorooctanoic acid and 2,4-dinitrophenol) to evaluate mixing and inputs of water and contaminants from tributaries into the mainstem of the transboundary Danube River. Stable isotope (delta O-18, delta H-2) variations from low values (- 13.3 parts per thousand, - 95.1 parts per thousand) in the Upper Danube after the Inn River confluence to high values (- 9.9 parts per thousand, - 69.7 parts per thousand) at the Danube River mouth revealed snowmelt dominated tributary mixing (- 70%) in the mainstem. Stable isotopes of nitrate (delta N-15-NO3) in the Danube River varied from lower values (+ 6.7 parts per thousand) in the Upper Danube to higher values after the mixing with Morava River (+10.5 parts per thousand) and showed that cold snowmelt can reduce biological activity and controls nitrate biotransformation processes in the mainstem up to 1000 km downstream. Data on emerging contaminants affirmed the low biodegradation potential of organic compounds transferred into the mainstem by tributaries. We found pollutant source tracing in large rivers is complicated by mixing of multiple sources with overlapping isotopic signatures, but additional tracers such as CECs improve the interpretation of hydrological processes (e.g., water transit time) and support tracing of nitrate pollution sources, and biogeochemical processes. Our approach can be applied to other watersheds to improve the understanding of dilution and mixing processes. Moreover, it provides directions for improving national and transboundary water quality monitoring networks.