Inland rivers are hotspots of anthropogenic indirect nitrous oxide (N 2 O) emissions, but the underlying microbial processes remain poorly understood. This study measured N 2 O fluxes from agricultural and urban rivers in Taihu watershed and investigated the microbial processes driving N 2 O production and consumption. The N 2 O fluxes were significantly higher in agricultural rivers (140.1 ± 89.1 μmol m -2 d -1 ) than in urban rivers (25.1 ± 27.0 μmol m -2 d -1 ) ( p < 0.001). All wind-based models significantly underestimated N 2 O flux in urban rivers ( p < 0.05) when using the Intergovernmental Panel on Climate Change method because they underestimated the N 2 O emission factor (EF 5r ). Wind speed and nitrate were the key factors affecting N 2 O fluxes in agricultural and urban rivers, respectively. NirK -type denitrifiers produced N 2 O in urban river water, while nirS -type denitrifiers consumed N 2 O in the sediments of all rivers. Co-occurrence network analysis indicated organics from Microcystis served as electron donors for denitrifiers (dominated by Flavobacterium ) in water, while direct interspecies electron transfer between Thiobacillus and methanogens and between Dechloromonas and sulfate-reducing bacteria enhanced N 2 O reduction in sediments. This study advances our knowledge on the distinctive microbial processes that determine N 2 O emissions in inland rivers and illustrates the need to revise EF 5r for N 2 O estimation in urban rivers.