[en] Highlights: • Source apportionment and transboundary flux of contaminants in the Red River. • USA was the major source of atrazine into Canada, but not neonicotinoids. • Levels of atrazine and neonicotinoids pose minimal risk to aquatic organisms. • Pharmaceuticals found at elevated levels downstream of wastewater inputs. • PFAS and ARGs found throughout with no evidence of any significant point-sources. The Red River originates in the U.S., drains into Lake Winnipeg, and is a significant pathway for nutrients. We investigate its role as a source for pesticides, pharmaceuticals, per- and polyfluoroalkyl substances (PFASs), and microbes bearing antibiotic resistance genes (ARGs). We delineate agricultural, urban, and rural land-use for organic contaminants to determine the extent of chemical transboundary riverine fluxes, and characterize levels and trends of organic contaminants and ARGs between spring and fall 2014 and 2015. The herbicide atrazine peaked at over 500 ng/L (14-day time-weighted average) near the border, indicating that the U.S. represents the major source into Canada from the Red River. Neonicotinoid insecticides had relatively constant concentrations, suggesting more widespread agricultural use in both countries. Pesticide concentrations were greatest post-application in June and July. Mass loadings of pesticides over the sampling periods, from the river to Lake Winnipeg, ranged from approximately 800 kg of atrazine, to 120 kg of thiamethoxam and clothianidin, to 40 kg of imidacloprid. Exposure distributions for atrazine exceeded benchmark water quality guidelines for protection of aquatic life (0.2% probability of exceeding chronic benchmark) with no exceedances for neonicotinoids. Seven pharmaceuticals were detected, mostly at low ng/L levels downstream of the City of Winnipeg wastewater treatment plant. Carbamazepine, the only pharmaceutical detected consistently at all sites, contributed on average 20 kg each year into Lake Winnipeg. While minor inputs were observed all along the river, city inputs represented the greatest source of pharmaceuticals to the river. Both PFASs and ARGs were observed consistently and ubiquitously, indicative of an anthropogenically-influenced system with no indications of any single point-source signature. While transboundary flux from the U.S. was an important source of pesticides to the Red River, especially for atrazine, observed concentrations of all measured contaminants suggest that known aquatic toxicological risk is minimal.