BackgroundRivers and streams are one of the primary sources of nitrous oxide (N2O) which is an important greenhouse gas with great global warming potential. Yet, over the past century, human activities have dramatically increased reactive nitrogen loadings into and consequently led to increased N2O emission from the river ecosystems. Here, we carried out a study in two subtropical rivers, i.e., Jinshui River and Qi River with slight and intense human disturbance in their respective catchments in China. The study intended to explore spatial variability and seasonality in N2O emissions, and the relative importance of physicochemical variables, nitrification and denitrification potentials, and functional genes abundance influencing N2O emissions.ResultsN2O concentration, N2O saturation, and N2O flux of Jinshui River peaked in high flow season. N2O concentration, N2O saturations, and N2O flux in Qi River and downstream of Jinshui River were significantly higher than that in other areas in normal and low flow seasons. N2O concentration was positively correlated with water temperature, water NO3−, and DOC, negatively correlated with water NH4+ and DOC/NO3− (the ratio of dissolved organic carbon to NO3− in water), and positively correlated with potential nitrification rate in high flow season, but not correlated with functional genes abundance. Both rivers had lower N2O saturation and flux than many freshwater systems, and their EFr-5 (N2O emission factor for river) was lower than the recommended values of IPCC.ConclusionsWhile the two rivers were moderate sources of N2O and N2O emissions in river systems were normally elevated in the summer, areas with intense human disturbance had higher N2O concentration, N2O saturations, and N2O flux than those with slight human disturbance. Physicochemical variables were good indicators of N2O emissions in the river ecosystems.