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Background Conversion of leached and runoff nitrate (NO3–) from agricultural land into emissions of the greenhouse gas (GHG) nitrous oxide (N2O) by denitrification in water bodies has to be reported in national GHG inventories. The global IPCC default methodology for estimating these indirect N2O emissions assumes that a fixed fraction of nitrogen (N) inputs (Fracleach) is lost through leaching and runoff. However, this method does not consider all relevant country‐specific conditions that may influence NO3– leaching. Aims The aim of this study was to apply a model‐based approach for estimating indirect N2O emissions through NO3– leaching and runoff from agricultural soils for use in Germany's national GHG inventory. Methods High‐resolution spatial data and a comprehensive model system (RAUMIS‐mGROWA‐DENUZ) were used to derive regionally differentiated and temporarily dynamic Fracleach values from N surplus and hydrogeological conditions. These were then used to estimate indirect N2O emissions in accordance with the IPCC methodology. Results The nationwide average of the new implied Fracleach values was 0.099 kg N (kg N input)−1 in 2019. The new estimate of indirect N2O emissions was 10.4 Gg N2O in 1990 and 5.7 Gg N2O in 2019, which are 27 and 52% less than the calculation based on the 2006 IPCC Tier 1 methodology. Conclusions The model‐based method for estimating Fracleach incorporates relevant factors that influence NO3– leaching and runoff and considers site‐specific, spatially varying conditions and differences in the agrarian structure. The use of N surplus as the model driver allows annual changes in cropping conditions and the effects of N‐regulating policies and mitigation measures to be represented.

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