<p>Nitrate pollution in water bodies is a widespread environmental issue, yet studies focusing on the traceability of riverine nitrate pollution under facility agricultural systems are limited. Using a combination of water chemistry analysis, isotope techniques (δ¹⁵N-NO₃^-, δ¹⁸O-NO₃^-, δ²H-H₂O, and δ¹⁸O-H₂O), land use data, and Bayesian isotope mixing models (MixSIAR), this study conducted the first comprehensive investigation into the sources and transformations of NO₃^- in the Mihe River, a prominent greenhouse vegetable production area in Weifang, while also estimating the proportional contributions of each nitrate source to the river’s water. Results indicated that surface water samples were predominantly characterized by Ca²⁺-HCO₃^- composition during the wet period, whereas in the dry season, they primarily exhibited a Ca²⁺-Mg²⁺-Cl^--SO₄^2- composition. Sample sites within the Industrial Area (IA), Urban Area (UA) and Agricultural Area (AA) had higher NO₃^--N concentrations. In the Mihe River, nitrification was found to be the dominant nitrogen transformation process, with denitrification playing a secondary role. δ¹⁵N-NO₃^- and δ¹⁸O-NO₃^- analyses indicated that NO₃^- originated primarily from manure and sewage (MS) and soil organic nitrogen (SON), rather than from chemical fertilizers (CF). The MixSIAR model estimated that during the dry season, nitrate sources were primarily manure and sewage (62.0%), followed by soil organic nitrogen (25.9%) and chemical fertilizers (11.9%). During the wet period, manure and sewage accounted for 42.5%, soil organic nitrogen for 37.2%, and chemical fertilizers for 19.8% of the NO₃^- sources. These findings provide valuable insights for urban sustainability and NO₃^- pollution control</p> Graphical Abstract <p></p>