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Indirect N2O emissions from agricultural nitrogen (N) leaching and runoff in water bodies contribute significantly to the global atmospheric N2O budget. However, considerable uncertainty regarding this source remains in the bottom-up N2O inventory. Indirect N2O emission factor associated with N leaching and runoff (EF5: kg N2O-N per kg of NO3--N) incorporate three components for groundwater and surface drainage (EF5g), rivers (EF5r), and estuaries (EF5e). The 2006 IPCC default EF5 value was based on a small number of studies available at the time. Here we present the synthesis of 254 measurements of EF5, dissolved N2O, and nitrate from 106 studies. Our results do not support the further downward revision of EF5g by the IPCC and suggest an upward revision of EF5g of 0.0060. The emission factors for groundwater and springs (0.0079) was higher than that for surface drainage (0.0040). The emission factor for lakes, ponds, and reservoirs was 0.0012, whereas that for rivers was 0.0030, and a combined EF5r was 0.0026. Estimated EF5r and EF5e (0.0026) values from the study were close to the current IPCC default values (0.0025 each). We estimated an updated default EF5 value of 0.01 for the refinement of IPCC guidelines. (C) 2018 Elsevier Ltd. All rights reserved.