Although eutrophic urban rivers receiving loads of wastewater represent an important anthropogenic source of N2O, little is known as to how temperature and other environmental factors affect temporal variations in N2O emissions from wastewater treatment plants (WWTPs) and downstream rivers. Two-year monitoring at a WWTP and five river sites was complemented with available water quality data, laboratory incubations, and stable isotopes in N2O and NO3− to explore how wastewater effluents interact with seasonal changes in environmental conditions to affect downstream metabolic processes and N2O emissions from the lower Han River traversing the megacity Seoul. Water quality data from four WWTPs revealed significant inverse relationships between water temperature and the concentrations or fluxes of total N (TN) in effluents. Increased TN fluxes at low temperatures concurred with N2O surges in WWTP effluents and downstream rivers, counteracting the long-term decline in TN fluxes resulting from enhanced wastewater treatments. Incubation experiments with river water and sediment, in isolation or combined, implied the hypoxic winter sediment as a large source of N2O, whereas the anoxic summer sediment produced a smaller amount of N2O only when it was added with oxic water. For both WWTP effluents and downstream rivers, bulk isotope ratios and intramolecular distribution of 15N in N2O distinctly differed between summer and winter, indicating incomplete denitrification in the hypoxic sediment at low temperatures as a primary downstream source adding to WWTP-derived N2O. Winter surges in wastewater TN and sediment N2O release highlight temperature variability as an underappreciated control over anthropogenic N2O emissions from increasingly urbanized river systems worldwide.