In life cycle assessment (LCA), simple models are currently used to estimate cropping system nitrogen (N) emissions on farms. At large spatial scales (e.g., countries), these models are valid. At a smaller spatial scale (e.g., territories), these models may be less accurate, since they completely or partially ignore local conditions such as management practices, soil or climate. The purpose of this study was to consider the variability of those factors when estimating N emissions in LCA at the watershed scale. To this end, Syst'N, decision-support software based on a simulation model of crop and soil N dynamics at field and crop-rotation scales, was applied to predict N emissions from cropping systems in a coastal watershed (Lieue de Grève, France). Syst'N predictions were compared to N emissions estimated by AGRIBALYSE, a static site-dependent method at field and single-crop scales. Syst'N was more sensitive to site-specific soil properties than AGRIBALYSE. Estimates of N emissions that include spatial variability in soil and climate therefore become possible in LCA when a simulation model such as Syst'N is used in the inventory phase.